Hello,
I am getting the following error when building Amber and would appreciate pointers how to proceed:
[ 11%] Creating directories for 'PerlMol'
[ 11%] Performing download step for 'PerlMol'
[ 11%] No update step for 'PerlMol'
[ 11%] No patch step for 'PerlMol'
[ 11%] Performing configure step for 'PerlMol'
Checking if your kit is complete...
Looks good
Warning: prerequisite Chemistry::Mol 0.33 not found.
ERROR from evaluation of /uufs/chpc.utah.edu/sys/srcdir/r8/amber/24/amber24_src/build/AmberTools/src/PerlMol-0.3500/build/Chemistry-File-VRML-0.10/Makefile.PL: Could not open 'lib/Chemistry/File/VRML.pm': No such file or directory at /usr/share/perl5/vendor_perl/ExtUtils/MM_Unix.pm line 2920.
Verbose error is like this:
cd /uufs/chpc.utah.edu/sys/srcdir/r8/amber/24/amber24_src/build/AmberTools/src/PerlMol-0.3500/build && /uufs/chpc.utah.edu/sys/installdir/r8/cmake/3.26.0/bin/cmake -E env PERL5LIB=/uufs/chpc.utah.edu/sys/srcdir/r8/amber/24/amber24_src/build/AmberTools/src/PerlMol-0.3500/build /usr/bin/perl Makefile.PL PREFIX=/uufs/chpc.utah.edu/sys/srcdir/r8/amber/24/amber24_src/build/AmberTools/src/PerlMol-0.3500/install LIB=/uufs/chpc.utah.edu/sys/srcdir/r8/amber/24/amber24_src/build/AmberTools/src/PerlMol-0.3500/install/lib/perl INSTALL_BASE=
Checking if your kit is complete...
Looks good
Checking if your kit is complete...
Warning: the following files are missing in your kit:
lib/Chemistry/File/VRML.pm
t/pod.t
t/vrml.t
Please inform the author.
Warning: prerequisite Chemistry::Mol 0.33 not found.
ERROR from evaluation of /uufs/chpc.utah.edu/sys/srcdir/r8/amber/24/amber24_src/build/AmberTools/src/PerlMol-0.3500/build/Chemistry-File-VRML-0.10/Makefile.PL: Could not open 'lib/Chemistry/File/VRML.pm': No such file or directory at /usr/share/perl5/vendor_perl/ExtUtils/MM_Unix.pm line 2920.
make[2]: *** [AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir/build.make:92: AmberTools/src/PerlMol-0.3500/src/PerlMol-stamp/PerlMol-configure] Error 2
I am doing this on am HPC cluster running fairly stock Rocky Linux 8, with gcc/11.2.0, cuda/12.4.0, openmpi/5.0.3 and intel-oneapi-mkl/2024.0.0, all installed with Spack and loaded via modules. Perl is the stock OS.
The cmake command is as follows:
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
though I get the same error if I don't use MPI and CUDA.
Thanks,
Martin
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Received on Fri Oct 11 2024 - 09:00:02 PDT
