Dear Dustin,
If you can let us know your exact machine specs it would be easier to help.
Operating system, CPU, compiler versions etc.
For the moment I will assume you are using the Intel compilers on Linux P4
as this is probably one of the more common setups.
> labs computers. The commands I used to install: ./configure
> -mpi & make parallel after that I cd ../test make test, all
> of the installation works no errors.
First off. Do you need to run the program in parallel? If this is the first
time you have used the program and you want it for learning purposes, and/or
your machine is not part of a cluster / multi processor system then you do
NOT want to build a parallel version. Hence you can just do ./configure
without the MPI command. You can also specify some other options for
configure to tailor it more closely to your machine. I always recommend
building static and if you are on a pentium 4 using ifort you can do:
Export AMBERHOME=/export/shared_apps/amber8-new/
Export MKL_HOME=/export/shared_apps/intel/mkl72
cd $AMBERHOME
cd src
../configure -p4 -static ifort
make clean
make
cd $AMBERHOME/test
make
Manually check the any tests that show possible failures, it should just be
minor roundoff differences.
Then you should be able to run sander successfully.
> nohup sander -O -i mdin -o ER_TAM_solv_mini.out -p
> ../PREP/ER_TAM_solvate.top -c ../PREP/ER_TAM_solvate.crd -r
> ER_TAM_solv_mini.rst -ref ../PREP/ER_TAM_solvate.crd &
>
> The output:
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> libc.so.6 001AFF79 Unknown Unknown Unknown
This is probably due to the fact that you are trying to run a parallel
version of sander without MPI. Parallel versions need to be run with mpirun
-np x sander where x is the number of cpus... For the time being I would
stick to serial runs. In this case you would use the command:
nohup $AMBERHOME/exe/sander -O -i mdin -o ER_TAM_solv_mini.out -p
.../PREP/ER_TAM_solvate.top -c ../PREP/ER_TAM_solvate.crd -r
ER_TAM_solv_mini.rst -ref ../PREP/ER_TAM_solvate.crd &
Always check nohup.out and your ouptut file ER_TAM_solv_mini.out if the
program crashed to see what any error messages are.
I hope this helps.
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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Received on Wed Apr 13 2005 - 21:53:01 PDT
