pgf90 segfault

Accelerated Computing HPC Compilers Legacy PGI Compilers
1

Hello,

When compiling WRF 3.4 on ubuntu 12.04 LTS 64bit with PGI 12.6 I get the following:

pgf90 -r4 -i4 -O3  -w -Mfree -byteswapio   -o wrf_io.o  -I/admin/software/precise/pgi-12.6/netcdf-fortran-4.2/include -I../ioapi_share -c wrf_io.f
pgf90-Fatal-/nfs/admin/software/precise/pgi-12.6/linux86-64/12.6/bin/pgf901 TERMINATED by signal 11
Arguments to /nfs/admin/software/precise/pgi-12.6/linux86-64/12.6/bin/pgf901
/nfs/admin/software/precise/pgi-12.6/linux86-64/12.6/bin/pgf901 wrf_io.f -opt 3 -terse 1 -inform severe -nohpf -nostatic -x 19 0x400000 -quad -x 59 4 -x 59 4 -x 15 2 -x 49 0x400004 -x 51 0x20 -x 57 0x4c -x 58 0x10000 -x 124 0x1000 -x 57 0xfb0000 -x 58 0x78031040 -x 70 0x6c00 -x 47 0x400000 -x 48 4608 -x 49 0x100 -x 120 0x200 -stdinc /nfs/admin/software/precise/pgi-12.6/linux86-64/12.6/include:/usr/local/include:/usr/lib/gcc/x86_64-linux-gnu/4.6/include:/usr/lib/gcc/x86_64-linux-gnu/4.6/include:/usr/include -def unix -def __unix -def __unix__ -def linux -def __linux -def __linux__ -def __NO_MATH_INLINES -def __x86_64 -def __x86_64__ -def __LONG_MAX__=9223372036854775807L -def '__SIZE_TYPE__=unsigned long int' -def '__PTRDIFF_TYPE__=long int' -def __THROW= -def __extension__= -def __amd_64__amd64__ -def __k8 -def __k8__ -def __SSE__ -def __MMX__ -def __SSE2__ -def __SSE3__ -def __STDC_HOSTED__ -idir /admin/software/precise/pgi-12.6/netcdf-fortran-4.2/include -idir ../ioapi_share -nofreeform -i4 -x 125 2 -vect 48 -y 54 1 -y 124 0x8 -freeform -modexport /tmp/pgf90VWvfnHzScsnA.cmod -modindex /tmp/pgf90NWvf1Qfd9XW0.cmdx -output /tmp/pgf903WvfL8P3qeCY.ilm
make[3]: [wrf_io.o] Error 127 (ignored)

Has anyone seen this before? Thanks!

2

Hi Richard,

I tried to recreate this error here, but unfortunately it worked fine for me. Can you tell me a bit more about your build. What configuration are you using (serial, smpar, dmpar)? Are you using NetCDF or PNetCDF?

Thanks,
Mat

3

Hi Mat,

I’m building serial WRF. NetCDF is netcdf-fortran-4.2. Here’s a few other things I’ve compiled that are also in the LD_LIBRARY_PATH:

Currently Loaded Modulefiles:

  1. pgi-12.6/linux86-64 3) pgi-12.6/hdf4-4.2.7-patch1 5) pgi-12.6/szip-2.1 7) pgi-12.6/udunits-2.1.24
  2. pgi-12.6/hdf5-1.8.9 4) pgi-12.6/jpeg-8b 6) pgi-12.6/udunits-1.12.11 8) pgi-12.6/netcdf-fortran-4.2

I’m currently downloading 12.8 and I will try to compile WRF again after installing it. Do you think I need to recompile all of the other libraries as well?

4

I’m building serial WRF. NetCDF is netcdf-fortran-4.2

That’s the same as me. Normally this would be an indication of a UMR but valgrind doesn’t show anything. Another possibility is a stack overflow. What’s your shell’s stack limit?

I’m currently downloading 12.8 and I will try to compile WRF again after installing it. Do you think I need to recompile all of the other libraries as well?

12.8 is worth a try but I don’t see any related issue in the fixed TPR list. You shouldn’t need to recompile the other libraries.

  • Mat
5

It was 8192. I tried compiling it again with 12.8, both with stacksize 8192 and unlimited, and it still segfaults in the same place.

Do you think it’s NetCDF related? This is the first part in the WRF compile where it attempts to include netcdf.

Thanks,
Richard

6

Hi,

I’m wondering if there was any indication of the error that caused this problem? I also get pgfortran to segfault with ubuntu 12.04, though this is a homegrown code and I’m using the 12.10 (latest?) version of pgf.

7

Hi Charles,

Can you send a report to PGI Customer Service (trs@pgroup.com) and include a example that reproduces the problem? We don’t have any similar open issues, so you may have encountered a new problem. Though, we would neeed to replicate the issue here in order to determine the cause.

Thanks,
Mat