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【求助】，Linux Cluster下ADF 2007递交任务的脚本
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xujc1983
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苦逼青椒一枚
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2楼2008-04-01 19:32:55
y1ding
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3楼2008-04-01 19:53:06
y1ding
铁杆木虫 (著名写手)
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★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
lei0736(金币+2,VIP+0):真有心 谢谢
lei0736(金币+10,VIP+0):转移
lei0736(金币+2,VIP+0):真有心 谢谢
lei0736(金币+10,VIP+0):转移
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ADF 2007.01 The Amsterdam Density Functional (ADF) package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers worldwide in such diverse fields as pharmaco-chemistry and materials science. It is currently particularly popular in the research areas of: . Homogeneous and heterogeneous catalysis . Inorganic chemistry . Heavy element chemistry . Various types of spectroscopy . Biochemistry For further details please check the official website for the software, www.scm.com. ADF Availability@SERC: SERC has recently upgraded ADF software from version 2005.01 to 2007.01. The software is installed on SGI-Altix3700 (hostname: altix) and five SUN AMD Opteron based machines (hostnames: sunlx1_3 to sunlx1_7). The software is node-locked to these machines and hence the user can use the software only on these machines. Modules of ADF on SUN machines: ADF version 2007.99 BAND version 2007.99 ADFGUI version 2007.99 BANDGUI version 2007.99 GUI version 2007.99 Utils version 2007.99 ADF on these machines can be used to generate the ADF input files using appropriate GUIs. ADF jobs that need to use only a single processor can be submitted on the machines using PBSPro software. Module of ADF on SGI-Altix machine: ADF version 2007.99 BAND version 2007.99 Utils version 2007.99 SGI-Altix only supports compute modules of ADF. Users can submit parallel ADF jobs on this machine using PBSPro software. Procedure to use ADF SOFTWARE: Environment settings on SGI-Altix machine: (Example for csh/tcsh) setenv ADFHOME /home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01 setenv ADFBIN /home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01/bin setenv ADFRESOURCES /home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01/atomicdata setenv SCMLICENSE /home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01/license.txt Environment settings on SUN Opteron machines: setenv ADFHOME /home/pkg/lic/chemistry/adf/linux-em64/adf2007.01 setenv ADFBIN /home/pkg/lic/chemistry/adf/linux-em64/adf2007.01/bin setenv ADFRESOURCE /home/pkg/lic/chemistry/adf/linux-em64/adf2007.01/atomicdata setenv SCMLICENSE /home/pkg/lic/chemistry/adf/linux-em64/adf2007.01/license.txt One has to create a run file for using adf or band. Sample run scripts for band and adf are $ADFHOME/examples directory Using ADF on altix: On altix users have to submit jobs to PBS job scheduler. Users have to create a script file to submit to PBS batch system. Below is an example script that can be used to submit an ADF job using 8 cpus. -----------File myjob.sh------------------------------------- #!/bin/sh #PBS -l ncpus=8 ADFHOME=/home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01 ADFBIN=/home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01/bin ADFRESOURCES=/home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01/atomicdata SCMLICENSE=/home/pkg/lic/chemistry/adf/linux-ia64/adf2007.01/license.txt nproc=8 cd / ${ADFBIN}/adf -n ${nproc} -----------End of file myjob.sh------------------------------- This myjob.sh job script may be submitted to pbs using qsub command. Please note that the shell variable "nproc" has to be set equal to the number of processors that adf is going to use and this has also got to be equal to the "ncpus" PBS directive. Using ADF on sunlx machines: On the sunlx machines adf jobs can use only one cpu and are to be submitted through PBS. You may run adfGUI/bandGUI interactively on sunlx1_3 to sunlx1_7 machines locally. Below is an example script that can be used to submit an ADF job that is expected to consume approximately 16 hours of cpu-time. -----------File myjob.sh------------------------------------- #!/bin/sh #PBS -l cput=16:00:00 #PBS -l select=1:ADF=True ADFHOME=/home/pkg/lic/chemistry/adf/linux-em64/adf2007.01 ADFBIN=/home/pkg/lic/chemistry/adf/linux-em64/adf2007.01/bin ADFRESOURCES=/home/pkg/lic/chemistry/adf/linux-em64/adf2007.01/atomicdata SCMLICENSE=/home/pkg/lic/chemistry/adf/linux-em64/adf2007.01/license.txt nproc=1 cd / ${ADFBIN}/adf -n ${nproc} -----------End of file myjob.sh------------------------------- This myjob.sh job script may be submitted to pbs using qsub command. Please note that the shell variable "nproc" has to be set equal to the one for these machines. For any problems or help please contact HelpDesk@SERC by E-mail or phone (#444 within SERC). |
4楼2008-04-01 19:56:23
y1ding
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5楼2008-04-01 19:57:08
y1ding
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★
lei0736(金币+1,VIP+0):谢谢
lei0736(金币+1,VIP+0):谢谢
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Laboratory for Molecular Simulation- [ 翻译此页 BETA ]Running ADF and ADF-BAND on cosmos. To run the newest version of ADF/ADF-BAND on cosmos, you will need to add the following lines to your pbs job file: ... www.chem.tamu.edu/LMS/adf.html - 12k - 网页快照 - 类似网页 |
6楼2008-04-01 19:58:29
zhangfq7112
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7楼2008-04-04 10:58:32
suntao1982
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8楼2008-04-04 20:52:41
zhangfq7112
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9楼2008-04-05 18:26:39
10楼2008-04-25 15:02:08