AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Mar 12 2007 - 05:51:38 CST

the key thing is the message "this test not set up for parallel".
so, the way to fix the problem is to not run that test with parallel.

On 3/12/07, Mostafa Sadighi <sadighi_amb_at_yahoo.com> wrote:
> 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
> in.md: 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
> libc.so.6 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 (127.0.0.1) 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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>
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