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:
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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
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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://coffee.sdsc.edu/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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- Department of Chemisty - -
- 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 Sun Jun 11 2006 - 06:07:19 PDT
