Greetings.
Just installed AmberTools which ended up in a directory amber18. We do
not at this time have a license for Amber 18. Did this:
TOPDIR=/usr/common/modules/el7/x86_64/software/amber/19-CentOS-vanilla
mkdir -p $TOPDIR
export PATH=/opt/ompi401/bin:$PATH #or it cannot figure out which
mpi, fails in fftw
./configure --python-install local -mpi --with-python /usr/bin/python
--prefix $TOPDIR gnu
#let it apply available patches
make 2>&1 | tee build_2019_09_23.log
#it was installed into $TOPDIR
export AMBERHOME=$TOPDIR
export DO_PARALLEL='/opt/ompi401/bin/mpirun -n 4'
. $TOPDIR/amber.sh
make test 2>&1 | tee tests_2019_09_23.log
# 1032 file comparisons passed
# 154 file comparisons failed (0 ignored)
# 89 tests experienced errors
# Test log file saved as
/usr/common/modules/el7/x86_64/software/amber/19-CentOS-vanilla/logs/test_at_parallel/2019-09-23_11-41-26.log
# Test diffs file saved as
/usr/common/modules/el7/x86_64/software/amber/19-CentOS-vanilla/logs/test_at_parallel/2019-09-23_11-41-26.diff
# unclear if all the failures are because of no Amber 18 or something
else.
Why so many errors? The 154 all correspond to "possible FAILURE" lines.
I'm not sure where the 89 are. Did I do something wrong in this
install? It is a CentOS 7 system.
The diff file listed above has only "<" lines, suggesting that the
corresponding output files in the test were empty.
The first failure seen was this:
Parallel test with trajectory offset requires Parallel NetCDF.
Cpptraj was compiled without Parallel NetCDF support.
Skipped test: Parallel test with trajectory offset
********************************************************************************
TEST: /usr/common/src/amber18/AmberTools/src/cpptraj/test/Test_Strip
CPPTRAJ: One frame strip command test
[1] Error: Process is handling less than 1 frame. Try reducing #
processes.
[2] Error: Process is handling less than 1 frame. Try reducing #
processes.
[3] Error: Process is handling less than 1 frame. Try reducing #
processes.
Error: Error(s) occurred during execution.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[41297,1],0]
Exit code: 1
--------------------------------------------------------------------------
/usr/common/modules/el7/x86_64/software/amber/19-CentOS-vanilla/bin/cpptraj.MPI:
Program error
possible FAILURE: file dummy.pdb.1 does not exist.
Thanks,
David Mathog
mathog.caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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Received on Mon Sep 23 2019 - 13:30:02 PDT
