Dear Amber developer:We are trying to install Amber14 on our system but we are
having hard time doing that. I'm attaching the log file of the compiling to the
e-mail.Here is the information about the compiler & MPI we used and the
OS:Compiler: GCC 4.8.2, OpenMPI 1.8.1OS: Redhat 6.5We have followed the
instructions outlined in
http://jswails.wikidot.com/installing-amber14-and-ambertools14We started with
serial with gnu compilation and finished off with the
make test . Afterwards we tried the parallel with gnu compiler and then
we received errors. We experienced errors when testing amber14 with serial code
in particular the cpptraj executable had some errors. For some reason
cpptraj was looking at libstdc++.so.6 in intel version when the
compiler is set to gcc. It should be looking at
<gcc-home-dir>/lib64/libstdc++.so.6 These errors are outlined in
ambercompile.log file.
We noticed there was an error with ptraj executable when compiling in
parallel, so we tried to compile ptraj manually
$AMBERHOME/AmberTools/src/ptraj using make. The Makefile required
pnetcdf.h in $AMBERHOME/amber14/include which was not present so we
created the file and took the content from the web. We recompiled ptraj
again and it failed again. When we tried to test SANDER it worked fine;
however, SANDER.MPI did not work and gave errors.
../../../bin/cpptraj:
/usr/global/intel/composer_xe/2015.0.090/vtune_amplifier_xe_2015.1.0.367959/lib64/libstdc++.so.6:
version `GLIBCXX_3.4.15' not found (required by ../../../bin/cpptraj)
./runmd.sh: Program error
make[3]: [ntx5] Error 1 (ignored)
Netcdf MD restart read test, ntx=1
diffing md1.rst7 with md2.rst7
PASSED
==============================================================
diffing ene1 with ene2
PASSED
==============================================================
../../../bin/cpptraj:
/usr/global/intel/composer_xe/2015.0.090/vtune_amplifier_xe_2015.1.0.367959/lib64/libstdc++.so.6:
version `GLIBCXX_3.4.15' not found (required by ../../../bin/cpptraj)
./runmd.sh: Program error
make[3]: [ntx1] Error 1 (ignored)
make[3]: Leaving directory
`/gpfs/apps/x86_64-rhel6/gcc-4.8.x/openmpi-1.8.x/amber14/test/netcdf'
cd csurften & ./Run.csurften_z-dir
diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir
Here is the error produced when trying to run sander.MPI:MD Simulation
job started on lionxv96.hpc.rcc.psu.edu at Thu Apr 2 13:23:34 EDT 2015
sander.MPI: symbol lookup error: /usr/global/gcc-4.8.x/openmpi/1.8.1/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weig
hts_empty
Any idea what could be wrong with the steps we followed to do the compilation?
Thank you very much for your help in this.
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814)863 8703
Fax (814)865 7927
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Received on Thu Apr 02 2015 - 11:30:02 PDT
