Hi there,
I'm trying to tackle building amber20 using the new cmake-based system for
the first time. I'm not sure what compiler to use, so am playing with GCC
11.2 on Rocky 8 Linux and have hit a problem.
The build process adds an RPATH into its test executables, with /usr/lib64
placed sufficiently near the start that the OS-provided GCC gfortran
runtime overrides my compiler (which is in a non-standard location). The
contents of $AMBERHOME/{bin,lib} don't suffer from this problem.
Manually deleting the RPATH fixes the test executables, but is annoying.
e.g.
$ readelf -d ./AmberTools/test/nab/rismala-mdiis0 | grep RPATH
0x000000000000000f (RPATH) Library rpath: [/local/slurm.1052/amber20/lib:/usr/lib64:/apps/developers/libraries/openblas/0.3.18/1/gcc-11.2/lib:/apps/developers/compilers/gcc/11.2/1/default/lib64:/lib64:/local/slurm.1052/amber20_src/build/AmberTools/src/xblas/build]
$ ./AmberTools/test/nab/rismala-mdiis0
./AmberTools/test/nab/rismala-mdiis0: /usr/lib64/libgfortran.so.5: version `GFORTRAN_10' not found (required by ./AmberTools/test/nab/rismala-mdiis0)
./AmberTools/test/nab/rismala-mdiis0: /usr/lib64/libgfortran.so.5: version `GFORTRAN_10' not found (required by /local/slurm.1052/amber20/lib/libnetcdff.so.6)
./AmberTools/test/nab/rismala-mdiis0: /usr/lib64/libgfortran.so.5: version `GFORTRAN_10' not found (required by /local/slurm.1052/amber20/lib/libpbsa.so)
$ chrpath -d ./AmberTools/test/nab/rismala-mdiis0
$ ./AmberTools/test/nab/rismala-mdiis0
getpdb: can't open file ala.pdb
$ echo $LD_LIBRARY_PATH
/local/slurm.1052/amber20/lib:/local/slurm.1052/amber20/lib:/apps/developers/libraries/openblas/0.3.18/1/gcc-11.2/lib:/apps/developers/libraries/openmpi/4.1.1/1/gcc-11.2/lib:/apps/developers/compilers/gcc/11.2/1/default/lib64:/apps/developers/compilers/gcc/11.2/1/default/lib:/apps/infrastructure/slurm/default/default/default/lib:/apps/infrastructure/slurm/default/default/default/lib:
$ echo $LIBRARY_PATH
/apps/developers/libraries/openblas/0.3.18/1/gcc-11.2/lib:/apps/developers/libraries/openmpi/4.1.1/1/gcc-11.2/lib:/apps/developers/compilers/gcc/11.2/1/default/lib64:/apps/developers/compilers/gcc/11.2/1/default/lib:/apps/infrastructure/slurm/default/default/default/lib:/apps/infrastructure/slurm/default/default/default/lib:/apps/infrastructure/slurm/default/default/default/lib:
Starting again and giving cmake "-DCMAKE_SKIP_INSTALL_RPATH=TRUE" results
in the same issue. Using "-DCMAKE_SKIP_RPATH=TRUE" causes the build to
fail, with the "make" step no longer being able find bundled libraries it
has built (e.g. netcdf)
Any tips, please? Or should I just be using intel or clang anyway?
Thanks,
Mark
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Received on Mon Nov 22 2021 - 09:30:02 PST
