Did anyone compile the parallel version of AMBER9 on a single CPU machine
using the latest mpich? I am having some weird problems with it. Here is
what I have done:
I compiled mpich-1.2.7 with 'ssh'. Everything went fine. Then I have
compiled the parallel version of AMBER9. I did not have any problems while
compiling it. I created a machine file for mpich.
The thing is, when I run 'mpirun', it is trying to use 'rsh' rather 'ssh'.
I checked the following to see which one was used in mpirun:
[yildirim.anatolia ~]# grep RSHCOMMAND /programs/mpich/bin/mpirun
RSHCOMMAND="ssh"
So, mpirun should be using ssh, but in reality it was trying to use rsh. I
renamed /usr/bin/rsh, and then created a link to /usr/bin/rsh to use
/usr/bin/ssh.
ln -s /usr/bin/ssh /usr/bin/rsh
The parallel test cases was working fine after this.
Did anyone have any problem like this? I could not find any answers on
this in the net.
Best,
On Fri, 9 Jun 2006, Ilyas Yildirim wrote:
> Dear All,
>
> In the AMBER 9 Manual, pp. # 8, it says that we can build the parallel
> ver. of AMBER 9 for a machine with a single CPU. My linux box is a single
> CPU P4 machine (SUSE 9.1 operating system). I have installed the parallel
> version by following the installation protocols. When I try to test the
> test cases, it is giving the following error:
> -------------------------------------------------------------------------
> ==============================================================
> cd bintraj; ./Run.bintraj
>
> sander and ptraj: test sander netCDF output and ptraj netCDF input
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_19949: p4_error: : 1
> ./Run.bintraj: Program error
> make[1]: [test.sander.BASIC] Error 1 (ignored)
> make[1]: Leaving directory `/programs/amber9/test'
> export TESTsander=/home/yildirim/amber9/exe/sander.MPI; cd 4096wat;
> ./Run.column_fft
> diffing mdout.column_fft.save with mdout.column_fft
> PASSED
> ==============================================================
> export TESTsander=/home/yildirim/amber9/exe/sander.MPI; cd jar_multi;
> ./Run.jar
> Error: specified more groups ( 2 ) than the number of
> processors (
> 1 ) !
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_20101: p4_error: : 1
> ./Run.jar: Program error
> make: *** [test.sander.BASIC.MPI] Error 1
> -------------------------------------------------------------------------
> In the manual (the same page), it is saying that free energy calculations
> can be done if the parallel ver. of AMBER 9 is compiled in a single CPU
> machine. I saw in Ross Walker's following website that he compiled
> the single CPU sander.MPI for SDSC (Datastar):
>
> http://www.rosswalker.co.uk/amber_sdsc/datastar.htm
>
> Maybe I am doing something wrong with the compilation, but during the
> parallel version compilation, I did not get any error messages. I will
> appreciate if someone can comment on the error message I am getting.
>
> Best,
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
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- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Jun 14 2006 - 06:07:12 PDT
