Building OPENCMISS Iron after setting up arch path raises problem with gdcm #187

vraj004 · 2019-11-24T03:30:17Z

I tried to compile opencmiss iron (ubuntu 18.04, gcc-9, gfortran 9) by first setting up arch path:

cd setup-build
cmake -DOPENCMISS_ROOT=../opencmiss -DOPENCMISS_LIBRARIES=iron
.-DOPENCMISS_PERFORM_INITIAL_BUILD=False ./setup
make VERBOSE=1
cd ../../build/manage/release

cmake .

make create_config
make build_config

The compiler fails at OC_GDCM:

Scanning dependencies of target OC_GDCM-ABI
[ 15%] Creating directories for 'OC_GDCM-ABI'
[ 17%] No download step for 'OC_GDCM-ABI'
[ 17%] No patch step for 'OC_GDCM-ABI'
[ 17%] No update step for 'OC_GDCM-ABI'
[ 17%] Performing configure step for 'OC_GDCM-ABI'
-- OC_GDCM-ABI configure command succeeded. See also /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-configure-*.log
[ 17%] Performing build step for 'OC_GDCM-ABI'
CMake Error at extproj/stamp/OC_GDCM-ABI-build-Release.cmake:49 (message):
Command failed: 2

'/usr/local/bin/cmake' '--build' '/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release' '--' '-j8'

See also

/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-build-*.log

CMakeFiles/OC_GDCM-ABI.dir/build.make:114: recipe for target '/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-build' failed
make[6]: *** [/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-build] Error 1
CMakeFiles/Makefile2:3104: recipe for target 'CMakeFiles/OC_GDCM-ABI.dir/all' failed

The text was updated successfully, but these errors were encountered:

vraj004 · 2019-11-24T03:34:06Z

Further examination of the compiler error inside the gdcm-abi folder:
[ 7%] Built target gdcmCommon
[ 7%] Building CXX object Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/gdcmCReader.cxx.o
In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h:21,
from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmFile.h:19,
from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmReader.h:19,
from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Wrapping/C/gdcmCReader.cxx:12:
/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmElement.h:606:26: error: declaration of ‘class gdcm::Element<4096, TVM>’ ambiguates earlier template instantiation for ‘class gdcm::Element<4096, 218367>’ [-fpermissive]
606 | template class Element<VR::OB, TVM>;
| ^~~~~~~~~~~~~~~~~~~~
/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmElement.h:612:26: error: declaration of ‘class gdcm::Element<16384, TVM>’ ambiguates earlier template instantiation for ‘class gdcm::Element<16384, 218367>’ [-fpermissive]
612 | template class Element<VR::OW, TVM>;
| ^~~~~~~~~~~~~~~~~~~~
/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmElement.h:612:26: error: declaration of ‘class gdcm::Element<16384, TVM>’ ambiguates earlier template instantiation for ‘class gdcm::Element<4096, 218367>’ [-fpermissive]
Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/build.make:62: recipe for target 'Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/gdcmCReader.cxx.o' failed
make[2]: *** [Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/gdcmCReader.cxx.o] Error 1
CMakeFiles/Makefile2:113: recipe for target 'Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/all' failed
make[1]: *** [Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/all] Error 2
M

chrispbradley · 2019-11-24T03:45:59Z

Hi Vijay,
yes, whilst gcc-9 fixes the internal compiler fault it brings in additional problems in that some of the external libraries do not build with it because they are too old. GDCM above is not required by iron so you can turn it off. Indeed, go to your configs directory and edit OpenCMISSLocalConfig.cmake and set

set(OC_USE_CLANG OFF)
set(OC_USE_CSIM OFF)
set(OC_USE_LLVM OFF)
set(OC_USE_ZINC OFF)
set(CELLML_WITH_CSIM NO)

It should then build with gcc-9

vraj004 · 2019-11-24T05:11:03Z

Why does this error not pop up when setting up opencmiss iron with the default settings - without setting the arch paths?

vraj004 · 2019-11-24T05:28:27Z

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’:
lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57:
/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory
194 | #include <mpi.h>
| ^~~~~~~
compilation terminated.
make[9]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1
make[8]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2
make[8]: *** Waiting for unfinished jobs....
make[7]: *** [all] Error 2

sgenie68 · 2019-11-24T06:03:11Z

What MPI do you use there? Gene

…

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 18:28, Vijay Rajagopal wrote: After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH: lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include <mpi.h> | ^~~~~~~ compilation terminated. make[9]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: *** Waiting for unfinished jobs.... make[7]: *** [all] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDRU5UONSEPXW3LQQEDQVIGHZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAEEIY#issuecomment-557859363>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDTT4DO5U2MFRHFGISDQVIGHZANCNFSM4JQ5FI5Q>.

vraj004 · 2019-11-24T06:18:59Z

Mpich Get Outlook for Android<https://aka.ms/ghei36>

________________________________ From: sgenie68 <[email protected]> Sent: Sunday, November 24, 2019 5:03:12 PM To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>; Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) What MPI do you use there? Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 24/11/19 18:28, Vijay Rajagopal wrote: After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH: lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include <mpi.h> | ^~~~~~~ compilation terminated. make[9]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: *** Waiting for unfinished jobs.... make[7]: *** [all] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDRU5UONSEPXW3LQQEDQVIGHZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAEEIY#issuecomment-557859363>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDTT4DO5U2MFRHFGISDQVIGHZANCNFSM4JQ5FI5Q>.

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chrispbradley · 2019-11-24T07:52:41Z

Why does this error not pop up when setting up opencmiss iron with the default settings - without setting the arch paths?

Hi Vijay, I'll speculate that when you do the setup you specify iron only libraries and therefore it doesn't build zinc and therefore the zinc dependencies.

chrispbradley · 2019-11-24T07:54:50Z

Hi Vijay,
It can't find mpich for some reason. What do you get when you do a which mpiexec? mpif90 --version? mpicc --version? Also have you installed libmpich-dev?

vraj004 · 2019-11-24T08:45:53Z

Hi Chris I have installed libmpich-dev. I get gcc-9 when checking version of mpicc and mpif90. I get the following error for mpiexec: [mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided [mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed [mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: Chris Bradley <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Sunday, 24 November 2019 at 6:55 pm To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Hi Vijay, It can't find mpich for some reason. What do you get when you do a which mpiexec? mpif90 --version? mpicc --version? Also have you installed libmpich-dev? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZP4P2ELAAIZXXJSCBTQVIXMXA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAFYSY#issuecomment-557866059>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZPVANIOPNABYHXAFODQVIXMXANCNFSM4JQ5FI5Q>.

chrispbradley · 2019-11-24T09:28:47Z

Hi Vijay,
is that output for

which mpiexec

or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH?

sgenie68 · 2019-11-24T09:35:05Z

The problem might be related to the conflicts between anaconda-installed version of mpich and the system-configured one Gene

…

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 22:28, Chris Bradley wrote: Hi Vijay, is that output for which mpiexec or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDWQVVZBYCYFFNQ5QDTQVJCNBA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAHFKQ#issuecomment-557871786>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDU34U2UCCBALLOLKXLQVJCNBANCNFSM4JQ5FI5Q>.

vraj004 · 2019-11-24T09:37:19Z

HI Gene, I am now running a linux virtual machine without anaconda. So this is an issue on linux ubuntu 18.04 Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Sunday, 24 November 2019 at 8:35 pm To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) The problem might be related to the conflicts between anaconda-installed version of mpich and the system-configured one Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 24/11/19 22:28, Chris Bradley wrote: Hi Vijay, is that output for which mpiexec or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDWQVVZBYCYFFNQ5QDTQVJCNBA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAHFKQ#issuecomment-557871786>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDU34U2UCCBALLOLKXLQVJCNBANCNFSM4JQ5FI5Q>.

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vraj004 · 2019-11-24T09:39:44Z

HI Chris, I did env | grep PATH and this is what I get: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin The previous output was for running mpiexec. I ran mpiexec--version and this is what I get: HYDRA build details: Version: 3.3a2 Release Date: Sun Nov 13 09:12:11 MST 2016 CC: gcc -Wl,-Bsymbolic-functions -Wl,-z,relro CXX: g++ -Wl,-Bsymbolic-functions -Wl,-z,relro F77: gfortran -Wl,-Bsymbolic-functions -Wl,-z,relro F90: gfortran -Wl,-Bsymbolic-functions -Wl,-z,relro Configure options: '--disable-option-checking' '--prefix=/usr' '--build=x86_64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--libexecdir=${prefix}/lib/x86_64-linux-gnu' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-libfabric' '--enable-shared' '--enable-fortran=all' '--disable-rpath' '--disable-wrapper-rpath' '--sysconfdir=/etc/mpich' '--libdir=/usr/lib/x86_64-linux-gnu' '--includedir=/usr/include/mpich' '--docdir=/usr/share/doc/mpich' '--with-hwloc-prefix=system' '--enable-checkpointing' '--with-hydra-ckpointlib=blcr' 'CPPFLAGS= -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/mpich-O9at2o/mpich-3.3~a2/src/mpl/include -I/build/mpich-O9at2o/mpich-3.3~a2/src/mpl/include -I/build/mpich-O9at2o/mpich-3.3~a2/src/openpa/src -I/build/mpich-O9at2o/mpich-3.3~a2/src/openpa/src -D_REENTRANT -I/build/mpich-O9at2o/mpich-3.3~a2/src/mpi/romio/include' 'CFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security -O2' 'CXXFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security -O2' 'FFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -O2' 'FCFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -O2' 'build_alias=x86_64-linux-gnu' 'MPICHLIB_CFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security' 'MPICHLIB_CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'MPICHLIB_CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security' 'MPICHLIB_FFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong' 'MPICHLIB_FCFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'FC=gfortran' 'F77=gfortran' 'MPILIBNAME=mpich' '--cache-file=/dev/null' '--srcdir=.' 'CC=gcc' 'LIBS=' 'MPLLIBNAME=mpl' Process Manager: pmi Launchers available: ssh rsh fork slurm ll lsf sge manual persist Topology libraries available: hwloc Resource management kernels available: user slurm ll lsf sge pbs cobalt Checkpointing libraries available: blcr Demux engines available: poll select Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: Chris Bradley <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Sunday, 24 November 2019 at 8:28 pm To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Hi Vijay, is that output for which mpiexec or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZIED5HX4LMO52VUM3DQVJCNBA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAHFKQ#issuecomment-557871786>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZJDAYUMDA3FIFZQAHTQVJCNBANCNFSM4JQ5FI5Q>.

sgenie68 · 2019-11-24T21:47:38Z

Hi, Vijay Could you give me the command line you used when you ran mpiexec? Cheers, Gene

…

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 21:45, Vijay Rajagopal wrote: HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

vraj004 · 2019-11-24T21:49:29Z

I simply typed: mpiexec Best wishes Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Hi, Vijay Could you give me the command line you used when you ran mpiexec? Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 24/11/19 21:45, Vijay Rajagopal wrote: HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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sgenie68 · 2019-11-24T21:57:54Z

Vijay, can you configure MPICH without BLCR or any other checkpointing support? Gene

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On 25/11/19 10:49, Vijay Rajagopal wrote: I simply typed: mpiexec Best wishes Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Hi, Vijay Could you give me the command line you used when you ran mpiexec? Cheers, Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html> On 24/11/19 21:45, Vijay Rajagopal wrote: > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > values failed — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>.

vraj004 · 2019-11-24T22:01:37Z

I simply installed libmpich-dev via sudo apt install libmpich-dev What else should I do? Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, can you configure MPICH without BLCR or any other checkpointing support? Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 10:49, Vijay Rajagopal wrote: I simply typed: mpiexec Best wishes Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Hi, Vijay Could you give me the command line you used when you ran mpiexec? Cheers, Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> On 24/11/19 21:45, Vijay Rajagopal wrote: > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > values failed — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>.

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sgenie68 · 2019-11-24T22:17:55Z

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo: sudo mpiexec Cheers, Gene

…

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On 25/11/19 11:01, Vijay Rajagopal wrote: I simply installed libmpich-dev via sudo apt install libmpich-dev What else should I do? Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, can you configure MPICH without BLCR or any other checkpointing support? Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html> On 25/11/19 10:49, Vijay Rajagopal wrote: > I simply typed: mpiexec > > Best wishes > > Vijay Rajagopal | Senior Lecturer > Department of Biomedical Engineering | Melbourne School of Engineering > Building 261, 197-203 Bouverie Street > The University of Melbourne, Victoria 3010 Australia > T: +61 3 834 41281 E: > ***@***.******@***.***> > Cell Structure and Mechanobiology > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> > > > From: sgenie68 ***@***.***> > Reply to: OpenCMISS/iron ***@***.***> > Date: Monday, 25 November 2019 at 8:47 am > To: OpenCMISS/iron ***@***.***> > Cc: Vijay Rajagopal ***@***.***>, Author > ***@***.***> > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > arch path raises problem with gdcm (#187) > > Hi, Vijay > > Could you give me the command line you used when you ran mpiexec? > > Cheers, > Gene > > -- > Scientific Software Specialist > Auckland Bioengineering Institute > The University of Auckland > e: ***@***.*** > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > w: > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> > > > On 24/11/19 21:45, Vijay Rajagopal wrote: > > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > > values failed > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on > GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, > or > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZIZKIQY6EUM6JZ7ARDQVL2GHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV5AY#issuecomment-557932163>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNKEGUOSXDYO2WHXI3QVL2GHANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDQBTMMQK6V52KIMHQDQVL2UDA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV7LQ#issuecomment-557932462>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDQGPIEAFPCERA4CVI3QVL2UDANCNFSM4JQ5FI5Q>.

vraj004 · 2019-11-25T01:44:59Z

Hi Gene, here it is: [mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided [mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed [mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo: sudo mpiexec Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 11:01, Vijay Rajagopal wrote: I simply installed libmpich-dev via sudo apt install libmpich-dev What else should I do? Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, can you configure MPICH without BLCR or any other checkpointing support? Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> On 25/11/19 10:49, Vijay Rajagopal wrote: > I simply typed: mpiexec > > Best wishes > > Vijay Rajagopal | Senior Lecturer > Department of Biomedical Engineering | Melbourne School of Engineering > Building 261, 197-203 Bouverie Street > The University of Melbourne, Victoria 3010 Australia > T: +61 3 834 41281 E: > ***@***.******@***.***> > Cell Structure and Mechanobiology > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>> > > > From: sgenie68 ***@***.***> > Reply to: OpenCMISS/iron ***@***.***> > Date: Monday, 25 November 2019 at 8:47 am > To: OpenCMISS/iron ***@***.***> > Cc: Vijay Rajagopal ***@***.***>, Author > ***@***.***> > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > arch path raises problem with gdcm (#187) > > Hi, Vijay > > Could you give me the command line you used when you ran mpiexec? > > Cheers, > Gene > > -- > Scientific Software Specialist > Auckland Bioengineering Institute > The University of Auckland > e: ***@***.*** > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > w: > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>> > > > On 24/11/19 21:45, Vijay Rajagopal wrote: > > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > > values failed > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on > GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, > or > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZIZKIQY6EUM6JZ7ARDQVL2GHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV5AY#issuecomment-557932163>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNKEGUOSXDYO2WHXI3QVL2GHANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDQBTMMQK6V52KIMHQDQVL2UDA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV7LQ#issuecomment-557932462>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDQGPIEAFPCERA4CVI3QVL2UDANCNFSM4JQ5FI5Q>.

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sgenie68 · 2019-11-25T01:48:17Z

Ok, you need to give it an executable - something that runs under mpi control, even a simple mpiexec -np 4 hostname would do Cheers, gene

…

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 25/11/19 14:45, Vijay Rajagopal wrote: Hi Gene, here it is: ***@***.*** set_default_values (ui/mpich/utils.c:1529): no executable provided ***@***.*** HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed ***@***.*** main (ui/mpich/mpiexec.c:149): error parsing parameters Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo: sudo mpiexec Cheers, Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html> On 25/11/19 11:01, Vijay Rajagopal wrote: > I simply installed libmpich-dev via sudo apt install libmpich-dev > > What else should I do? > > > > Vijay Rajagopal | Senior Lecturer > Department of Biomedical Engineering | Melbourne School of Engineering > Building 261, 197-203 Bouverie Street > The University of Melbourne, Victoria 3010 Australia > T: +61 3 834 41281 E: > ***@***.******@***.***> > Cell Structure and Mechanobiology > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> > > > From: sgenie68 ***@***.***> > Reply to: OpenCMISS/iron ***@***.***> > Date: Monday, 25 November 2019 at 8:58 am > To: OpenCMISS/iron ***@***.***> > Cc: Vijay Rajagopal ***@***.***>, Author > ***@***.***> > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > arch path raises problem with gdcm (#187) > > Vijay, can you configure MPICH without BLCR or any other checkpointing > support? > > Gene > > -- > Scientific Software Specialist > Auckland Bioengineering Institute > The University of Auckland > e: ***@***.*** > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > w: > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> > > > On 25/11/19 10:49, Vijay Rajagopal wrote: > > I simply typed: mpiexec > > > > Best wishes > > > > Vijay Rajagopal | Senior Lecturer > > Department of Biomedical Engineering | Melbourne School of Engineering > > Building 261, 197-203 Bouverie Street > > The University of Melbourne, Victoria 3010 Australia > > T: +61 3 834 41281 E: > > ***@***.******@***.***> > > Cell Structure and Mechanobiology > > > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > > > > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>> > > > > > > > From: sgenie68 ***@***.***> > > Reply to: OpenCMISS/iron ***@***.***> > > Date: Monday, 25 November 2019 at 8:47 am > > To: OpenCMISS/iron ***@***.***> > > Cc: Vijay Rajagopal ***@***.***>, Author > > ***@***.***> > > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > > arch path raises problem with gdcm (#187) > > > > Hi, Vijay > > > > Could you give me the command line you used when you ran mpiexec? > > > > Cheers, > > Gene > > > > -- > > Scientific Software Specialist > > Auckland Bioengineering Institute > > The University of Auckland > > e: ***@***.*** > > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > > w: > > > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>> > > > > > > > On 24/11/19 21:45, Vijay Rajagopal wrote: > > > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > > > values failed > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on > > > GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, > > > or > > > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > > <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, > > > or unsubscribe > > > <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>. > > > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on > GitHub<#187?email_source=notifications&email_token=AAGX4ZIZKIQY6EUM6JZ7ARDQVL2GHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV5AY#issuecomment-557932163>, > or > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNKEGUOSXDYO2WHXI3QVL2GHANCNFSM4JQ5FI5Q>. > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDQBTMMQK6V52KIMHQDQVL2UDA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV7LQ#issuecomment-557932462>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDQGPIEAFPCERA4CVI3QVL2UDANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZLYKZKD6ZFD7G6NIWLQVL4RJA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAWJ6A#issuecomment-557933816>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZJO7Y64Z2KK7DRIV3DQVL4RJANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDXPRVCMABVAHH6SPWDQVMUZZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFA3WBI#issuecomment-557955845>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDVZT3NVSDZJGW7GOWDQVMUZZANCNFSM4JQ5FI5Q>.

vraj004 · 2019-11-25T02:00:02Z

Yes, sorry that works Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Monday, 25 November 2019 at 12:48 pm To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Ok, you need to give it an executable - something that runs under mpi control, even a simple mpiexec -np 4 hostname would do Cheers, gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 14:45, Vijay Rajagopal wrote: Hi Gene, here it is: ***@***.*** set_default_values (ui/mpich/utils.c:1529): no executable provided ***@***.*** HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed ***@***.*** main (ui/mpich/mpiexec.c:149): error parsing parameters Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo: sudo mpiexec Cheers, Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> On 25/11/19 11:01, Vijay Rajagopal wrote: > I simply installed libmpich-dev via sudo apt install libmpich-dev > > What else should I do? > > > > Vijay Rajagopal | Senior Lecturer > Department of Biomedical Engineering | Melbourne School of Engineering > Building 261, 197-203 Bouverie Street > The University of Melbourne, Victoria 3010 Australia > T: +61 3 834 41281 E: > ***@***.******@***.***> > Cell Structure and Mechanobiology > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>> > > > From: sgenie68 ***@***.***> > Reply to: OpenCMISS/iron ***@***.***> > Date: Monday, 25 November 2019 at 8:58 am > To: OpenCMISS/iron ***@***.***> > Cc: Vijay Rajagopal ***@***.***>, Author > ***@***.***> > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > arch path raises problem with gdcm (#187) > > Vijay, can you configure MPICH without BLCR or any other checkpointing > support? > > Gene > > -- > Scientific Software Specialist > Auckland Bioengineering Institute > The University of Auckland > e: ***@***.*** > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > w: > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>> > > > On 25/11/19 10:49, Vijay Rajagopal wrote: > > I simply typed: mpiexec > > > > Best wishes > > > > Vijay Rajagopal | Senior Lecturer > > Department of Biomedical Engineering | Melbourne School of Engineering > > Building 261, 197-203 Bouverie Street > > The University of Melbourne, Victoria 3010 Australia > > T: +61 3 834 41281 E: > > ***@***.******@***.***> > > Cell Structure and Mechanobiology > > > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > > > > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>>> > > > > > > > From: sgenie68 ***@***.***> > > Reply to: OpenCMISS/iron ***@***.***> > > Date: Monday, 25 November 2019 at 8:47 am > > To: OpenCMISS/iron ***@***.***> > > Cc: Vijay Rajagopal ***@***.***>, Author > > ***@***.***> > > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > > arch path raises problem with gdcm (#187) > > > > Hi, Vijay > > > > Could you give me the command line you used when you ran mpiexec? > > > > Cheers, > > Gene > > > > -- > > Scientific Software Specialist > > Auckland Bioengineering Institute > > The University of Auckland > > e: ***@***.*** > > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > > w: > > > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>> > > > > > > > On 24/11/19 21:45, Vijay Rajagopal wrote: > > > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > > > values failed > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on > > > GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, > > > or > > > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > > <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, > > > or unsubscribe > > > <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>. > > > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on > GitHub<#187?email_source=notifications&email_token=AAGX4ZIZKIQY6EUM6JZ7ARDQVL2GHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV5AY#issuecomment-557932163>, > or > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNKEGUOSXDYO2WHXI3QVL2GHANCNFSM4JQ5FI5Q>. > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDQBTMMQK6V52KIMHQDQVL2UDA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV7LQ#issuecomment-557932462>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDQGPIEAFPCERA4CVI3QVL2UDANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZLYKZKD6ZFD7G6NIWLQVL4RJA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAWJ6A#issuecomment-557933816>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZJO7Y64Z2KK7DRIV3DQVL4RJANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDXPRVCMABVAHH6SPWDQVMUZZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFA3WBI#issuecomment-557955845>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDVZT3NVSDZJGW7GOWDQVMUZZANCNFSM4JQ5FI5Q>.

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sgenie68 · 2019-11-25T02:01:19Z

Good, now do: which mpiexec and see where it leads you to Gene

…

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 25/11/19 15:00, Vijay Rajagopal wrote: Yes, sorry that works Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 12:48 pm To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Ok, you need to give it an executable - something that runs under mpi control, even a simple mpiexec -np 4 hostname would do Cheers, gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html> On 25/11/19 14:45, Vijay Rajagopal wrote: > Hi Gene, here it is: > > > ***@***.*** set_default_values (ui/mpich/utils.c:1529): no > executable provided > > ***@***.*** HYD_uii_mpx_get_parameters > (ui/mpich/utils.c:1740): setting default values failed > > ***@***.*** main (ui/mpich/mpiexec.c:149): error parsing > parameters > > > > Vijay Rajagopal | Senior Lecturer > Department of Biomedical Engineering | Melbourne School of Engineering > Building 261, 197-203 Bouverie Street > The University of Melbourne, Victoria 3010 Australia > T: +61 3 834 41281 E: > ***@***.******@***.***> > Cell Structure and Mechanobiology > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> > > > From: sgenie68 ***@***.***> > Reply to: OpenCMISS/iron ***@***.***> > Date: Monday, 25 November 2019 at 9:18 am > To: OpenCMISS/iron ***@***.***> > Cc: Vijay Rajagopal ***@***.***>, Author > ***@***.***> > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > arch path raises problem with gdcm (#187) > > Vijay, sorry to bombard you with the questions - but can you try execute > mpiexec with sudo: > > sudo mpiexec > > Cheers, > Gene > > -- > Scientific Software Specialist > Auckland Bioengineering Institute > The University of Auckland > e: ***@***.*** > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > w: > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> > > > On 25/11/19 11:01, Vijay Rajagopal wrote: > > I simply installed libmpich-dev via sudo apt install libmpich-dev > > > > What else should I do? > > > > > > > > Vijay Rajagopal | Senior Lecturer > > Department of Biomedical Engineering | Melbourne School of Engineering > > Building 261, 197-203 Bouverie Street > > The University of Melbourne, Victoria 3010 Australia > > T: +61 3 834 41281 E: > > ***@***.******@***.***> > > Cell Structure and Mechanobiology > > > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > > > > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>> > > > > > > > From: sgenie68 ***@***.***> > > Reply to: OpenCMISS/iron ***@***.***> > > Date: Monday, 25 November 2019 at 8:58 am > > To: OpenCMISS/iron ***@***.***> > > Cc: Vijay Rajagopal ***@***.***>, Author > > ***@***.***> > > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > > arch path raises problem with gdcm (#187) > > > > Vijay, can you configure MPICH without BLCR or any other checkpointing > > support? > > > > Gene > > > > -- > > Scientific Software Specialist > > Auckland Bioengineering Institute > > The University of Auckland > > e: ***@***.*** > > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > > w: > > > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>> > > > > > > > On 25/11/19 10:49, Vijay Rajagopal wrote: > > > I simply typed: mpiexec > > > > > > Best wishes > > > > > > Vijay Rajagopal | Senior Lecturer > > > Department of Biomedical Engineering | Melbourne School of Engineering > > > Building 261, 197-203 Bouverie Street > > > The University of Melbourne, Victoria 3010 Australia > > > T: +61 3 834 41281 E: > > > ***@***.******@***.***> > > > Cell Structure and Mechanobiology > > > > > > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > > > > > > > > > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>>> > > > > > > > > > > > > From: sgenie68 ***@***.***> > > > Reply to: OpenCMISS/iron ***@***.***> > > > Date: Monday, 25 November 2019 at 8:47 am > > > To: OpenCMISS/iron ***@***.***> > > > Cc: Vijay Rajagopal ***@***.***>, Author > > > ***@***.***> > > > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > > > arch path raises problem with gdcm (#187) > > > > > > Hi, Vijay > > > > > > Could you give me the command line you used when you ran mpiexec? > > > > > > Cheers, > > > Gene > > > > > > -- > > > Scientific Software Specialist > > > Auckland Bioengineering Institute > > > The University of Auckland > > > e: ***@***.*** > > > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > > > w: > > > > > > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>> > > > > > > > > > > > > On 24/11/19 21:45, Vijay Rajagopal wrote: > > > > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > > > > values failed > > > > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on > > > > > > GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, > > > > > > or > > > > > > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. > > > > > > > > > > > > — > > > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > > > > > > <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, > > > > > > or unsubscribe > > > > > > <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>. > > > > > > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on > > > GitHub<#187?email_source=notifications&email_token=AAGX4ZIZKIQY6EUM6JZ7ARDQVL2GHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV5AY#issuecomment-557932163>, > > > or > > > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNKEGUOSXDYO2WHXI3QVL2GHANCNFSM4JQ5FI5Q>. > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > > <#187?email_source=notifications&email_token=AAGJIDQBTMMQK6V52KIMHQDQVL2UDA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV7LQ#issuecomment-557932462>, > > > or unsubscribe > > > <https://github.com/notifications/unsubscribe-auth/AAGJIDQGPIEAFPCERA4CVI3QVL2UDANCNFSM4JQ5FI5Q>. > > > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on > GitHub<#187?email_source=notifications&email_token=AAGX4ZLYKZKD6ZFD7G6NIWLQVL4RJA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAWJ6A#issuecomment-557933816>, > or > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZJO7Y64Z2KK7DRIV3DQVL4RJANCNFSM4JQ5FI5Q>. > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDXPRVCMABVAHH6SPWDQVMUZZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFA3WBI#issuecomment-557955845>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDVZT3NVSDZJGW7GOWDQVMUZZANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. 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vraj004 · 2019-11-25T02:59:43Z

Hi Gene, /usr/bin/mpiexec Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Monday, 25 November 2019 at 1:01 pm To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Good, now do: which mpiexec and see where it leads you to Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 15:00, Vijay Rajagopal wrote: Yes, sorry that works Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 12:48 pm To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Ok, you need to give it an executable - something that runs under mpi control, even a simple mpiexec -np 4 hostname would do Cheers, gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>> On 25/11/19 14:45, Vijay Rajagopal wrote: > Hi Gene, here it is: > > > ***@***.*** set_default_values (ui/mpich/utils.c:1529): no > executable provided > > ***@***.*** HYD_uii_mpx_get_parameters > (ui/mpich/utils.c:1740): setting default values failed > > ***@***.*** main (ui/mpich/mpiexec.c:149): error parsing > parameters > > > > Vijay Rajagopal | Senior Lecturer > Department of Biomedical Engineering | Melbourne School of Engineering > Building 261, 197-203 Bouverie Street > The University of Melbourne, Victoria 3010 Australia > T: +61 3 834 41281 E: > ***@***.******@***.***> > Cell Structure and Mechanobiology > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>> > > > From: sgenie68 ***@***.***> > Reply to: OpenCMISS/iron ***@***.***> > Date: Monday, 25 November 2019 at 9:18 am > To: OpenCMISS/iron ***@***.***> > Cc: Vijay Rajagopal ***@***.***>, Author > ***@***.***> > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > arch path raises problem with gdcm (#187) > > Vijay, sorry to bombard you with the questions - but can you try execute > mpiexec with sudo: > > sudo mpiexec > > Cheers, > Gene > > -- > Scientific Software Specialist > Auckland Bioengineering Institute > The University of Auckland > e: ***@***.*** > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > w: > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>> > > > On 25/11/19 11:01, Vijay Rajagopal wrote: > > I simply installed libmpich-dev via sudo apt install libmpich-dev > > > > What else should I do? > > > > > > > > Vijay Rajagopal | Senior Lecturer > > Department of Biomedical Engineering | Melbourne School of Engineering > > Building 261, 197-203 Bouverie Street > > The University of Melbourne, Victoria 3010 Australia > > T: +61 3 834 41281 E: > > ***@***.******@***.***> > > Cell Structure and Mechanobiology > > > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > > > > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>>> > > > > > > > From: sgenie68 ***@***.***> > > Reply to: OpenCMISS/iron ***@***.***> > > Date: Monday, 25 November 2019 at 8:58 am > > To: OpenCMISS/iron ***@***.***> > > Cc: Vijay Rajagopal ***@***.***>, Author > > ***@***.***> > > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > > arch path raises problem with gdcm (#187) > > > > Vijay, can you configure MPICH without BLCR or any other checkpointing > > support? > > > > Gene > > > > -- > > Scientific Software Specialist > > Auckland Bioengineering Institute > > The University of Auckland > > e: ***@***.*** > > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > > w: > > > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>> > > > > > > > On 25/11/19 10:49, Vijay Rajagopal wrote: > > > I simply typed: mpiexec > > > > > > Best wishes > > > > > > Vijay Rajagopal | Senior Lecturer > > > Department of Biomedical Engineering | Melbourne School of Engineering > > > Building 261, 197-203 Bouverie Street > > > The University of Melbourne, Victoria 3010 Australia > > > T: +61 3 834 41281 E: > > > ***@***.******@***.***> > > > Cell Structure and Mechanobiology > > > > > > Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| > > > > > > > > > twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal><http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>>>> > > > > > > > > > > > > From: sgenie68 ***@***.***> > > > Reply to: OpenCMISS/iron ***@***.***> > > > Date: Monday, 25 November 2019 at 8:47 am > > > To: OpenCMISS/iron ***@***.***> > > > Cc: Vijay Rajagopal ***@***.***>, Author > > > ***@***.***> > > > Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up > > > arch path raises problem with gdcm (#187) > > > > > > Hi, Vijay > > > > > > Could you give me the command line you used when you ran mpiexec? > > > > > > Cheers, > > > Gene > > > > > > -- > > > Scientific Software Specialist > > > Auckland Bioengineering Institute > > > The University of Auckland > > > e: ***@***.*** > > > p: +64 9 3737599 ext 89834 c: +64 21 840 825 > > > w: > > > > > > https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html><https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>>> > > > > > > > > > > > > On 24/11/19 21:45, Vijay Rajagopal wrote: > > > > HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default > > > > values failed > > > > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on > > > > > > GitHub<#187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377>, > > > > > > or > > > > > > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q>. > > > > > > > > > > > > — > > > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > > > > > > <#187?email_source=notifications&email_token=AAGJIDRLPCIVLTDSY4NIY2TQVLZGTA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVYCA#issuecomment-557931528>, > > > > > > or unsubscribe > > > > > > <https://github.com/notifications/unsubscribe-auth/AAGJIDRIBAMD6NVPAJFROTTQVLZGTANCNFSM4JQ5FI5Q>. > > > > > > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on > > > GitHub<#187?email_source=notifications&email_token=AAGX4ZIZKIQY6EUM6JZ7ARDQVL2GHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV5AY#issuecomment-557932163>, > > > or > > > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNKEGUOSXDYO2WHXI3QVL2GHANCNFSM4JQ5FI5Q>. > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > > <#187?email_source=notifications&email_token=AAGJIDQBTMMQK6V52KIMHQDQVL2UDA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAV7LQ#issuecomment-557932462>, > > > or unsubscribe > > > <https://github.com/notifications/unsubscribe-auth/AAGJIDQGPIEAFPCERA4CVI3QVL2UDANCNFSM4JQ5FI5Q>. > > > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on > GitHub<#187?email_source=notifications&email_token=AAGX4ZLYKZKD6ZFD7G6NIWLQVL4RJA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAWJ6A#issuecomment-557933816>, > or > unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZJO7Y64Z2KK7DRIV3DQVL4RJANCNFSM4JQ5FI5Q>. > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDXPRVCMABVAHH6SPWDQVMUZZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFA3WBI#issuecomment-557955845>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDVZT3NVSDZJGW7GOWDQVMUZZANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. 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sgenie68 · 2019-11-25T03:16:34Z

Vijay, can you run the following code before cmake: export FC=mpif90 export CC=mpicc export CXX=mpicxx and then run cmake stuff Cheers, Gene

…

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On 24/11/19 18:28, Vijay Rajagopal wrote: After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH: lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include <mpi.h> | ^~~~~~~ compilation terminated. make[9]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: *** Waiting for unfinished jobs.... make[7]: *** [all] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDRU5UONSEPXW3LQQEDQVIGHZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAEEIY#issuecomment-557859363>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDTT4DO5U2MFRHFGISDQVIGHZANCNFSM4JQ5FI5Q>.

vraj004 · 2019-11-25T23:07:26Z

The system stalls trying to find MPICH when I do that. Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: [email protected]<mailto:[email protected]> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 <[email protected]> Reply to: OpenCMISS/iron <[email protected]> Date: Monday, 25 November 2019 at 2:16 pm To: OpenCMISS/iron <[email protected]> Cc: Vijay Rajagopal <[email protected]>, Author <[email protected]> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, can you run the following code before cmake: export FC=mpif90 export CC=mpicc export CXX=mpicxx and then run cmake stuff Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 24/11/19 18:28, Vijay Rajagopal wrote: After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH: lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include <mpi.h> | ^~~~~~~ compilation terminated. make[9]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: *** Waiting for unfinished jobs.... make[7]: *** [all] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDRU5UONSEPXW3LQQEDQVIGHZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAEEIY#issuecomment-557859363>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDTT4DO5U2MFRHFGISDQVIGHZANCNFSM4JQ5FI5Q>.

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sgenie68 · 2019-11-26T01:43:20Z

Hi, Vijay Would it be possible to run cmake like that: strace cmake <arguments> 2>output_file and send this output file to me? Cheers, Gene

…

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: [email protected] p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 26/11/19 12:07, Vijay Rajagopal wrote: The system stalls trying to find MPICH when I do that. Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: ***@***.******@***.***> Cell Structure and Mechanobiology Group<https://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/>| twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal> From: sgenie68 ***@***.***> Reply to: OpenCMISS/iron ***@***.***> Date: Monday, 25 November 2019 at 2:16 pm To: OpenCMISS/iron ***@***.***> Cc: Vijay Rajagopal ***@***.***>, Author ***@***.***> Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187) Vijay, can you run the following code before cmake: export FC=mpif90 export CC=mpicc export CXX=mpicxx and then run cmake stuff Cheers, Gene -- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: ***@***.*** p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html> On 24/11/19 18:28, Vijay Rajagopal wrote: > After setting the corresponding flags off as suggested (in > OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH: > > lex.yy.c: In function ‘scotchyy_init_buffer’: > lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ > [-Wimplicit-function-declaration] > In file included from > /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: > /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: > fatal error: mpi.h: No such file or directory > 194 | #include <mpi.h> > | ^~~~~~~ > compilation terminated. > make[9]: *** > [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 > make[8]: *** [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 > make[8]: *** Waiting for unfinished jobs.... > make[7]: *** [all] Error 2 > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#187?email_source=notifications&email_token=AAGJIDRU5UONSEPXW3LQQEDQVIGHZA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAEEIY#issuecomment-557859363>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAGJIDTT4DO5U2MFRHFGISDQVIGHZANCNFSM4JQ5FI5Q>. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#187?email_source=notifications&email_token=AAGX4ZIUXEODHL2K745RR5LQVM7RHA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFA7AOA#issuecomment-557969464>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGX4ZNENVIG5OYZB4B3KBDQVM7RHANCNFSM4JQ5FI5Q>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#187?email_source=notifications&email_token=AAGJIDWHCIJNP44DAYLT2CLQVRLC7A5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFEDUEQ#issuecomment-558381586>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJIDVIQ7NC3Q4QCHZ4YW3QVRLC7ANCNFSM4JQ5FI5Q>.

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Building OPENCMISS Iron after setting up arch path raises problem with gdcm #187

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Building OPENCMISS Iron after setting up arch path raises problem with gdcm #187

Building OPENCMISS Iron after setting up arch path raises problem with gdcm #187

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