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shenghaisi金虫 (正式写手)
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大家可以看看这个问题，不知道desmond多cluster 并行如何做到？ Hello, I am a college student attempting a summer project of setting up a small computer cluster to run desmond. I have three machines (1) 4 core xeon (2) 6 core Phenom (3) 2 core Athlon So far, I have been able to setup a beowulf cluster with these machines and have MPI running successfully across all 12 cores. I have installed desmond all three machines. I have created a schrodinger.host file that looks like this #################################### # name: localhost host: athlon.helix.hpu.edu schrodinger: /usr/local/schrodinger2010 tmpdir: /usr/tmp processors: 2 # name: xeon host: xeon.helix.hp.edu schrodinger: /usr/local/schrodinger2010 tmpdir: /usr/tmp processors: 4 # name: phenom host: athlon.helix.hpu.edu schrodinger: /usr/local/schrodinger2010 tmpdir: /usr/tmp processors: 6 # ############################################ I am using the athlon machine as the machine for job submission. I can run desmond on individual machine but how do I specify desmond to run multisim on all 12 CPUs? Does the schrodinger.host file look correct? Sorry if this is a very basic question and I should be knowing this. Thanks for you help Hi , That looks good to me. However, when running Desmond across multiple machine without a queueng system like Torque, SGE, etc, you may find that the machines file for MPI is malformed in some cases. Because of this, I recommend that you change the names of your entries in the schrodinger.hosts file, so that they are resolvalbe on the network: #################################### # name: localhost host: athlon.helix.hpu.edu schrodinger: /usr/local/schrodinger2010 tmpdir: /usr/tmp processors: 2 # name: xeon host: xeon.helix.hp.edu schrodinger: /usr/local/schrodinger2010 tmpdir: /usr/tmp processors: 4 # name: athlon host: athlon.helix.hpu.edu schrodinger: /usr/local/schrodinger2010 tmpdir: /usr/tmp processors: 6 # ############################################ Here, I just changed the "name" parameter of the athlon.helix.hpu.edu machine so that it matched the FQDN (fully qualified domain name). This should ensure that the machines file (which is auto-generated by Desmond'd Job Control mechanism) is generated properly. Then, you launched the job using: $SCHRODINGER/utilities/multisim -HOST "xeon:2 althlon:2" -cpu 4 -mode umbrealla ... For more details on launching multisim from the command line, see the Desmond v2.4 User Manual. Best, James On May 20, 5:08 pm, raymond - 隐藏被引用文字 - - 显示引用的文字 - > Hello, I am a college student attempting a summer project of setting > up a small computer cluster to run desmond. I have three machines > (1) 4 core xeon > (2) 6 core Phenom > (3) 2 core Athlon > So far, I have been able to setup a beowulf cluster with these > machines and have MPI running successfully across all 12 cores. > I have installed desmond all three machines. I have created a > schrodinger.host file that looks like this > #################################### > # > name: localhost > host: athlon.helix.hpu.edu > schrodinger: /usr/local/schrodinger2010 > tmpdir: /usr/tmp > processors: 2 > # > name: xeon > host: xeon.helix.hp.edu > schrodinger: /usr/local/schrodinger2010 > tmpdir: /usr/tmp > processors: 4 > # > name: phenom > host: athlon.helix.hpu.edu > schrodinger: /usr/local/schrodinger2010 > tmpdir: /usr/tmp > processors: 6 > # > ############################################ > I am using the athlon machine as the machine for job submission. I > can run desmond on individual machine but how do I specify desmond to > run multisim on all 12 CPUs? Does the schrodinger.host file look > correct? Sorry if this is a very basic question and I should be > knowing this. > Thanks for you help |
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shenghaisi
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4楼2011-06-24 20:16:16
shenghaisi
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