[AMBER] problem with "make test.parallel" for AMBER12

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Mon, 16 Apr 2012 15:15:21 +0100


I have a problem running the tests for the parallel executables. (My
apologies if this is not an AMBER issue per se)

I have:
compiled & tested AMBER12 in serial (with success)
downloaded and compiled openmpi-1.5.4 (using "./configure_openmpi -gnu" in
compiled AMBER12 in parallel (with success, it seems)

Now, I'd like to test AMBER12 in parallel.
First, I tried simply doing:

make test

The first series of tests that run are in AmberTools/test/nab and
these tests are fine.
Then, when trying to run tests in AmberTools/test/mmpbsa_py I get a bunch
of errors like this:

make[3]: Entering directory
cd EstRAL_Files && ./Run.makeparms
This is not a parallel test.
cd 01_Generalized_Born && ./Run.GB
[curie.chm.bris.ac.uk:23918] [[32424,1],0] ORTE_ERROR_LOG: Data unpack
would read past end of buffer in file util/nidmap.c at line 371
[curie.chm.bris.ac.uk:23918] [[32424,1],0] ORTE_ERROR_LOG: Data unpack
would read past end of buffer in file base/ess_base_nidmap.c at line 62
[curie.chm.bris.ac.uk:23918] [[32424,1],0] ORTE_ERROR_LOG: Data unpack
would read past end of buffer in file ess_env_module.c at line 173
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_base_build_nidmap failed
  --> Returned value Data unpack would read past end of buffer (-26)
instead of ORTE_SUCCESS

This is unfortunate, but not really of great importance to me, as the
parallel executables of the AMBER12 programs (not AmberTools12) is what I'm
really after.
However, when I get to this stage, the process simply 'hangs' after:
make[2]: Entering directory `/export/users/chmwvdk/amber12/test'
export TESTsander=/users/chmwvdk/amber12/bin/sander.MPI; make -k
make[3]: Entering directory `/export/users/chmwvdk/amber12/test'
cd cytosine && ./Run.cytosine

It turns out that the cytosine test has run fine, writing up to 'section 4'
in the output file (values in cytosine/cytosine.out and
cytosine/cytosine.out.save are identical), but nothing happens after that.
In other words, the process seems to hang on getting the TIMINGS
information (section 5) in the output file.

I checked that my environment was OK (as far as I can tell), i.e.
$PATH contains $AMBERHOME/bin
'which mpirun' gives $AMBERHOME/bin/mpirun
'which mpicc' gives $AMBERHOME/bin/mpicc

This installation is on a cluster, and I'm not sure if it is set up to run
in parallel on the headnode, so I also made a PBS submission script (as
suggested in http://archive.ambermd.org/200701/0112.html ) and submitted
This is the submission script:

#PBS -l walltime=5:0:0,nodes=1:ppn=4
#PBS -q veryshort
#PBS -N parallel_test
#PBS -j oe

export DO_PARALLEL="mpirun -np 4 "
export AMBERHOME=/users/chmwvdk/amber12/
cd $AMBERHOME/test
make test.parallel

Essentially the same appears to happen - no output is obtained past section
4 of the first test, cytosine/cytosine.out (which is identical to to the
equivalent section in cytosine/cytosine.out.save). The job continues to be
'running' though. So, the run seems to hang on obtaining the timing
information (section 5)?

Strangely, when I run a simple job on my own system (i.e. replace "make
test.parallel" with a line with e.g. $AMBERHOME/bin/sander.MPI as
executable and the usual flags), then the job finishes as normal (without
errors) and I do get the full output including the timing information.
So, it appears that I can actually use sander.MPI without problems...

How can I solve this, so that I can use 'make test' (or similar) to run the
series of tests for the parallel executables?

As an aside, I notice that the 'header' of output files from AMBER12 still

          Amber 11 SANDER 2010

That should probably be updated...

Many thanks in advance,
AMBER mailing list
Received on Mon Apr 16 2012 - 07:30:03 PDT
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