Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory

From: David A Case <>
Date: Wed, 12 Jan 2022 09:05:41 -0500

On Wed, Jan 12, 2022, Manuel Fernandez Merino wrote:

>Error: LD_LIBRARY_PATH does not include $AMBERHOME/lib!

If you submitting the job via some queue environment, you may need to
set the LD_LIBRARY_PATH in the script itself, not just in your .bashrc file.

>(In an attempt to solve the LD_LIBRARY_PATH issue). When I launch any
>job in the cluster, I also get the notification that the LD_LIBRARY_PATH
>variable is not included in the environment because of a security issue,
>which I believe may have to do with this problem.

See above: modify your environment in the script. If you still get the
security issue message, you'll need to discuss that with those who
administer the cluster.

>cd nab && make -k test testrism

You may need to avoid testing parallel nab. Go to
$AMBERHOME/AmberTools/test and edit the Makefile to remove references to

>cd ../src/cpptraj/test && make -k test
>make[3]: Entering directory '/nfs/software/pcosma/el7.2/amber20/AmberTools/src/cpptraj/test'
>make test.complete summary
>make[4]: Entering directory '/nfs/software/pcosma/el7.2/amber20/AmberTools/src/cpptraj/test'
>[] PMIX ERROR: ERROR in file gds_ds12_lock_pthread.c at line 168

I've not seen this before. If you mainly want to use the cluster with MPI
for pmemd, try this:

    cd $AMBERHOME/test && make test.parallel.pmemd

You may still get errors, but at least they will be more relevant.


p.s.: it's worth asking if other people are using Amber on this HPC cluster.
They may have more specific advice.

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Received on Wed Jan 12 2022 - 06:30:03 PST
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