On Mon, Sep 23, 2019 at 4:19 PM David Mathog <mathog.caltech.edu> wrote:
> 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
>
Please try again without the `--prefix` option. It might not setup properly
for testing cpptraj.
Hai
#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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>
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Received on Mon Sep 23 2019 - 14:00:02 PDT
