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小木虫论坛-学术科研互动平台 » 计算模拟区 » 量子化学 » Linux应用 » mpirun并行运行问题
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刘志凌

木虫 (小有名气)

[求助] mpirun并行运行问题

我在集群上运行一个软件,本意要求它一次同时运行两个任务,但是每次它都只是运行一个任务,软件的作者解释是如下,不知有没有大侠能否指点一下迷津.先行谢谢了.
It appears that both mpi processes launched, but for some reason they launched independently of each other.  This means that neither process was aware of the other process, so both processes were doing the same things.  Both processes opened Test.inp and then tried to create this directory:

/home/Test/Gaussian/bestSavedStructures

One process succeded, and the other failed.  The one that failed printed "Couldn't create log files directory." in the .e file and immediately stopped.  The other kept going and made it to iteration 10, which was the predetermined stopping point.  There didn't seem to be any problems with the disk which is very good.  If you can figure out how to get the processes to see each other, you'll have a working program.

Upon launch, each process prints it's rank (or index) and the total number of processes.  This is what was printed during this run:
This is MPI process with rank 0.  Total MPI processes: 1
This is MPI process with rank 0.  Total MPI processes: 1

This is what it should have printed:
This is MPI process with rank 0.  Total MPI processes: 2
This is MPI process with rank 1.  Total MPI processes: 2

Please replace '-np 2' in pso.pbs with another option.  You might try '-hostfile nodes.txt' or '-cpus-per-rank 1'.  Or look at other options listed at http://www.open-mpi.org/doc/v1.4/man1/mpirun.1.php .  Hope that helps!
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好人一生平安
1楼 2012-10-29 20:31:29
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刘志凌

木虫 (小有名气)
作者的指示的那几个选项我都试过了,结果还是一次运行一个任务
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好人一生平安
2楼2012-10-29 20:32:28
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virtualzx

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引用回帖:
2楼: Originally posted by 刘志凌 at 2012-10-29 07:32:28
作者的指示的那几个选项我都试过了,结果还是一次运行一个任务

请给出你的命令行
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3楼2012-10-30 03:53:15
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刘志凌

木虫 (小有名气)
引用回帖:
3楼: Originally posted by virtualzx at 2012-10-30 03:53:15
请给出你的命令行...

#!/bin/bash
#PBS -N TestJob
#PBS -l nodes=2:ppn=8,walltime=0:30:00
#PBS -l mem=4GB
export LD_LIBRARY_PATH=/home/fan_group/openmpi/lib:$LD_LIBRARY_PATH
echo PBS_O_WORKDIR=$PBS_O_WORKDIR
echo PBS_ENVIRONMENT=$PBS_ENVIRONMENT
echo PBS_NODEFILE=$PBS_NODEFILE
echo cat $PBS_NODEFILE
cat $PBS_NODEFILE
echo $PBS_NODEFILE
echo HOSTNAME=`/bin/hostname`

# Create the nodes.txt file
# The next line writes one node per line and allows duplicate nodes
# Use this if you want one Gaussian job per processor.
# cp $PBS_NODEFILE /home/fan_group/lzhl/pso/Test/Gaussian/nodes.txt


# The next line writes one node per line and does NOT allow duplicate nodes.
# Use this if you want one Gaussian job per node with each job runing in parallel on multiple processors.
cat $PBS_NODEFILE | uniq > /home/fan_group/lzhl/pso/Test/Gaussian/nodes.txt

cd /home/fan_group/pso1.5.2
/opt/openmpi/bin/mpirun -np 2 ./pso -walltime 0:30:00 /home/fan_group/lzhl/pso/Test/Gaussian/Test.inp
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好人一生平安
4楼2012-11-05 10:30:44
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