Error With PB2NC Tool in MET make_test.log File

[jhicks14]

It's me again -- back with some more MET installation issues. I had a previous discussion that involved installation issues that have since been resolved. However, I am trying to now install the newest versions of MET (11.0.2) and METplus. I am able to get all the way to the compilation of MET, to the point where make test is run. I am also using a different Conda env than I was last time (/cpc/met/MET11/python-env).

I believe there is an issue with finding the correct version/location of the libgfortran file, which I have had issues with before.

For reference, the version of libgfortran (v5) that I would like installed is here: /cpc/met/MET11/python-env/lib

However, I believe version 5 of libgfortran is being used for compilation (just showing one of the lines of output):

ldd /cpc/home/jhicks/MET11/MET-11.0.0-beta3/bin/pb2nc

libgfortran.so.5 => /cpc/met/MET11/python-env/lib/libgfortran.so.5 (0x00007fa38983e000)

Here is the error I am getting in the make_test.log file:

FATAL ERROR (SEGFAULT): Process 37275 got signal 11 @ local time = 2023-04-12 22:38:04Z
FATAL ERROR (SEGFAULT): Look for a core file in /cpc/met/MET11/MET-11.0.2/MET-11.0.2/scripts
FATAL ERROR (SEGFAULT): Process command line: ../src/tools/other/pb2nc/pb2nc ../data/sample_obs/prepbufr/ndas.t00z.prepbufr.tm12.20070401.nr ../out/pb2nc/sampl
e_pb.nc config/PB2NCConfig_G212 -v 2
make[1]: *** [pb2nc] Segmentation fault (core dumped)
make[1]: Leaving directory `/cpc/met/MET11/MET-11.0.2/MET-11.0.2/scripts'
make: *** [test] Error 2

Here is my compile_MET_all.sh and environmental variable file that I pass in.

install_met_env.cpc2.txt
compile_MET_all.txt

[jprestop]

Hi @jhicks14. Could you please pass along your config.log file from MET? I agree that I think the problem lies where you said:

I believe there is an issue with finding the correct version/location of the libgfortran file, which I have had issues with before.

Do you remember how you solved this problem the last time and can you try that again?

[jhicks14]

Hi @jprestop

Looks like I'm still getting the same error. This is the output from ls /usr/lib64/ | grep gfortran:

libgfortran.so.1
libgfortran.so.1.0.0
libgfortran.so.3
libgfortran.so.3.0.0

compile_MET_all.txt
install_met_env.cpc2.attempt1.txt
config.log

[jprestop]

Hi @jhicks14. I just wanted to check in to be sure you ran the compile script with the install_met_env.cpc2.attempt1.txt file? I ask because the config.log file does not show the -L${ADDTL_DIR}/lib added to FC_LIBS, which we included in the install_met_env.cpc2.attempt1.txt file:

export FC_LIBS="-L${ADDTL_DIR}/lib -lgfortran"
export FLIBS="-L${ADDTL_DIR}/lib -lgfortran"

From config.log:

FC_LIBS='-lgfortran'
FLIBS='-L/usr/lib64/lib -lgfortran'

[jhicks14]

Hi @jprestop

I'm not sure what the issue is now. We just upgraded to the latest version of RedHat Linux, so this error could be due to that, but basically it no longer gets to the "make test" part of the install. The config.log file looks fine, but the error lies in the make.log file for MET. I ran this using the install_met_env.cpc2.attempt1.txt file.

Should I just re-run all of the prerequisite programs (e.g. comment out the bottom part of the install file that contains the env vars)?

compile_MET_all.txt
install_met_env.cpc2.attempt1.txt
config.log
make.log

[jprestop]

Hi @jhicks14. My apologies for my delayed response. I was out of the office. Upgrading to the latest version of RedHat Linux, could have caused problems. It's hard to say. Since you weren't experiencing these problems previously and I don't see anything obvious in the files you sent, please go ahead an reinstall all of the library dependencies as you suggested, by commenting out the bottom part of the env vars file (starting with MET_GSL and ending with MET_NETCDF) Also, please leave this line commented the whole time and see what happens.

export LD_LIBRARY_PATH=/cpc/met/MET11/$PYTHON_VER/lib

Please let us know how it goes.

[jhicks14]

Hi @jprestop

I reinstalled all of the library dependencies (i.e., commented out all of the bottom part of the env vars file), kept the line you mentioned commented out, and received an error compiling GSL (couldn't be found in /usr/lib64). Fortunately, I fixed this by commenting out this line:

export LDFLAGS=/usr/lib64:${LDFLAGS}

Then everything ran successfully with no errors in the make_test.log file!

Thanks again for the help!

[jprestop]

@jhicks14 Excellent! Thank you so much for letting us know. I'll go ahead and mark this as answered, close, and lock it to prevent future posts in this thread.