AMBER: The parallel test fails while sander.MPI seems to be installed correctly

From: Mostafa Sadighi <>
Date: Mon, 12 Mar 2007 04:43:14 -0700 (PDT)

Dear AMBER community,
  I have recently compiled serial and parallel versions of amber9 by using Intel compilers.
  ./configure -lam €“p4 ifort_x86_64
  While there were no problems in running the serial test, the parallel test fails with the following error:
  After running lamboot and cd to $AMBERHOME/test
  # setenv DO_PARALLEL 'mpirun -np 2'
  # make test.parallel
  export TESTsander=/programs/amber9/exe/sander.MPI; make test.sander.BASIC
  make[1]: Entering directory `/programs/amber9/test'
  cd dmp; ./Run.dmp
  This test not set up for parallel
   cannot run in parallel with #residues < #pes
  cd adenine; ./Run.adenine
  This test not set up for parallel
   cannot run in parallel with #residues < #pes
  cd cytosine; ./Run.cytosine Permission denied.
  forrtl: severe (47): write to READONLY file, unit 6, file /programs/amber9/test/cytosine/cytosine.out
  Image PC Routine Line Source
  sander.MPI 0000000000837B23 Unknown Unknown Unknown
  sander.MPI 00000000008359DE Unknown Unknown Unknown
  sander.MPI 000000000081A840 Unknown Unknown Unknown
  sander.MPI 00000000007D9A4B Unknown Unknown Unknown
  sander.MPI 00000000007D96B4 Unknown Unknown Unknown
  sander.MPI 0000000000806293 Unknown Unknown Unknown
  sander.MPI 00000000004DE94C Unknown Unknown Unknown
  sander.MPI 00000000004C048A Unknown Unknown Unknown
  sander.MPI 00000000004BB9C3 Unknown Unknown Unknown
  sander.MPI 0000000000406FAA Unknown Unknown Unknown 0000003E1A21C4CC Unknown Unknown Unknown
  sander.MPI 0000000000406EE9 Unknown Unknown Unknown
  One of the processes started by mpirun has exited with a nonzero exit
  code. This typically indicates that the process finished in error.
  If your process did not finish in error, be sure to include a "return
  0" or "exit(0)" in your C code before exiting the application.
  PID 4344 failed on node n0 ( with exit status 47.
    ./Run.cytosine: Program error
  make[1]: *** [test.sander.BASIC] Error 1
  make[1]: Leaving directory `/programs/amber9/test'
  make: *** [test.sander.BASIC.MPI] Error 2
  I have checked the results of a parallel simulation
  # mpirun €“np 2 sander.MPI
  with a serial one and observed nearly same results for both cases during 1-ns trajectories.
  Although sander.MPI seems to be installed correctly I still can not test the parallel programs in the way mentioned in the user manual.
  Does anyone know how can I fix the problem?
  Thanks in advance,
  Mostafa Sadighi

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Received on Wed Mar 14 2007 - 06:07:13 PDT
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