RE: AMBER: QMMM simulations

From: Ross Walker <>
Date: Tue, 27 Nov 2007 16:41:11 -0800

Dear Pankaj,
This is likely not specific to QMMM calculations but all parallel runs run
through a queuing system? Chances are you have library mismatches on the
compute nodes than what you used to compile with. Is the MPI installation
identical on all nodes? Are the exact same compilers installed? Is you
environment the same on the compute nodes as the node you compiled on?
Are they the same cpu version and stepping?
I suspect the problem is that the version of the Intel compilers used to
compile amber is different from the ones making it into LD_LIBRARY_PATH on
the compute nodes so I would start by checking here.
Note you need to use the exact same compilers for both the MPI installation
and the AMBER installation and then the lib directory for this compiler must
be available on all nodes in a cluster.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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From: [] On Behalf Of
Pankaj R. Daga
Sent: Tuesday, November 27, 2007 15:21
Subject: AMBER: QMMM simulations

Hi amber community,


I am trying to run one amber QMMM simulation using sander. When I run
minimization using single processor, the job runs fine. However, when I
submit the job using multiple processors, I get the error as shown below.




mpirun -np 4 /usr/local/appl/amber9/exe/sander.MPI -O -i -o
1rtd_min1.out -p 1rtd_box.prmtop -c 1rtd_box.inpcrd -r 1rtd_min.rst7


/usr/local/appl/amber9/exe/sander.MPI: symbol lookup error:
/usr/local/appl/amber9/exe/sander.MPI: undefined symbol: ?0_memcopyA

MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()

MPI: aborting job




The installation of amber9 was proper and According to Amber test results,
Amber 9 is functioning properly for single and multiple cpus. Could anybody
help me to figure out, where is the problem? The input file is as shown




Initial min of our structure QMMM


  imin=1, maxcyc=500, ncyc=200,

  cut=8.0, ntb=1, ntc=1, ntf=1,






  spin = 2



  qm_ewald=1, qm_pme=1





Please help me a way out.


Thanks and Regards




If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |


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Received on Wed Nov 28 2007 - 06:07:43 PST
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