<div dir="auto"><div>N.B., example mid-term questions:<div dir="auto">1. What SBATCH command will give you 3 nodes?</div><div dir="auto">2. What command creates your .machines file?</div><div dir="auto">3. What are your fastest and slowest nodes?</div><div dir="auto">4. Which nodes have the best communications.</div><div dir="auto"><br></div><div dir="auto">N.B., please don't post your answers -- just understand!<br><br><div data-smartmail="gmail_signature" dir="auto">_____<br>Professor Laurence Marks<br>"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi<br><a href="http://www.numis.northwestern.edu">www.numis.northwestern.edu</a></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Nov 13, 2020, 04:21 Laurence Marks <<a href="mailto:laurence.marks@gmail.com">laurence.marks@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto">Much of what you are requesting is problem/cluster specific, so there is no magic answer -- it will vary. Suggestions:<div dir="auto">1) Read the UG sections on .machines and parallel operation.</div><div dir="auto">2) Read the man page for your cluster job command (srun)</div><div dir="auto">3) Reread the UG sections.</div><div dir="auto">4) Read the example scripts, and understand (lookup) all the commands so you know what they are doing.</div><div dir="auto"><br></div><div dir="auto">It is really not that complicated. If you cannot master this by yourself, I will wonder whether you are in the right profession.<br><br><div data-smartmail="gmail_signature" dir="auto">_____<br>Professor Laurence Marks<br>"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi<br><a href="http://www.numis.northwestern.edu" target="_blank" rel="noreferrer">www.numis.northwestern.edu</a></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Nov 13, 2020, 03:24 Dr. K. C. Bhamu <<a href="mailto:kcbhamu85@gmail.com" target="_blank" rel="noreferrer">kcbhamu85@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-size:large">Dear All</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">I need your extensive help.</div><div class="gmail_default" style="font-size:large">I have tried to provide full details that can help you understand my requirement. In case I have missed something, please let me know.</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">I am looking for a job file for our cluster. The available jobs files on FAQs are not working. They give me</div><div class="gmail_default" style="font-size:large">.machine0 .machines .machines_current files only wherein .machines has # and the other two are empty.<br></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">The script that is working fine for Quantum Espresso for 44core partition is below</div><div class="gmail_default" style="font-size:large">#!/bin/sh<br>#SBATCH -J test #job name<br>#SBATCH -p 44core #partition name<br>#SBATCH -N 1 #node<br>#SBATCH -n 18 #core<br>#SBATCH -o %x.o%j<br>#SBATCH -e %x.e%j<br>export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so #Do not change here!!<br>srun ~/soft/qe66/bin/pw.x < <a href="https://urldefense.com/v3/__http://case.in__;!!Dq0X2DkFhyF93HkjWTBQKhk!GAoAiAGPo-P9rf1ZIm9YcQa-sF1GVFoIXYQ5SUQSFmUQH3oCvMobKrJ6gbDtT98andJs2Q$" rel="noreferrer noreferrer" target="_blank">case.in</a> > case.out<br></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">I have compiled Wien2k_19.2 on the Centos queuing system which has the head node of Centos kernel Linux 3.10.0-1127.19.1.el7.x86_64.</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">I used compilers_and_libraries_2020.2.254 , fftw-3.3.8 , libxc-4.34 for the installation.</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">The details of the nodes that I can use are as follows (I can login into these nodes with my user password):</div><div class="gmail_default" style="font-size:large">NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON </div><div class="gmail_default" style="font-size:large">elpidos 1 master idle 4 4:1:1 15787 0 1 (null) none <br>node01 1 72core allocated 72 72:1:1 515683 0 1 (null) none <br>node02 1 72core allocated 72 72:1:1 257651 0 1 (null) none <br>node03 1 72core allocated 72 72:1:1 257651 0 1 (null) none <br>node09 1 44core mixed 44 44:1:1 128650 0 1 (null) none <br>node10 1 44core mixed 44 44:1:1 128649 0 1 (null) none <br>node11 1 52core* allocated 52 52:1:1 191932 0 1 (null) none <br>node12 1 52core* allocated 52 52:1:1 191932 0 1 (null) none <br></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">The other nodes have a mixture of the kernel as below.</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large"> OS=Linux 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 <br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> OS=Linux 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 </div><div class="gmail_default" style="font-size:large"> OS=Linux 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC 2019 <br></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Your extensive help will improve my research productivity.</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Thank you very much.</div><div class="gmail_default" style="font-size:large">Regards</div><div class="gmail_default" style="font-size:large">Bhamu</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large"><b>Full details of the nodes are here:</b></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">NodeName=elpidos Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=4 CPULoad=0.06<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.250 NodeHostName=elpidos Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=15787 AllocMem=0 FreeMem=5597 Sockets=4 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=master <br> BootTime=2020-10-13T14:25:13 SlurmdStartTime=2020-10-13T14:25:26<br> CfgTRES=cpu=4,mem=15787M,billing=4<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node01 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=72 CPUTot=72 CPULoad=72.00<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.1 NodeHostName=node01 Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=515683 AllocMem=0 FreeMem=363362 Sockets=72 Boards=1<br> State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=72core <br> BootTime=2020-10-13T20:44:04 SlurmdStartTime=2020-10-14T05:44:23<br> CfgTRES=cpu=72,mem=515683M,billing=72<br> AllocTRES=cpu=72<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node02 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=72 CPUTot=72 CPULoad=71.92<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.2 NodeHostName=node02 Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=257651 AllocMem=0 FreeMem=142057 Sockets=72 Boards=1<br> State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=72core <br> BootTime=2020-10-13T20:44:04 SlurmdStartTime=2020-10-14T05:44:17<br> CfgTRES=cpu=72,mem=257651M,billing=72<br> AllocTRES=cpu=72<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node03 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=72 CPUTot=72 CPULoad=71.96<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.3 NodeHostName=node03 Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=257651 AllocMem=0 FreeMem=168118 Sockets=72 Boards=1<br> State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=72core <br> BootTime=2020-10-13T20:44:33 SlurmdStartTime=2020-10-14T05:43:35<br> CfgTRES=cpu=72,mem=257651M,billing=72<br> AllocTRES=cpu=72<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node04 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=20 CPULoad=0.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.4 NodeHostName=node04 Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=128664 AllocMem=0 FreeMem=126677 Sockets=20 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=20core <br> BootTime=2020-10-13T20:43:24 SlurmdStartTime=2020-10-14T05:42:43<br> CfgTRES=cpu=20,mem=128664M,billing=20<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node05 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=4 CPULoad=0.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.5 NodeHostName=node05 Version=20.02.3<br> OS=Linux 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 <br> RealMemory=64190 AllocMem=0 FreeMem=63350 Sockets=4 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=4core <br> BootTime=2020-10-29T11:34:18 SlurmdStartTime=2020-10-29T11:34:30<br> CfgTRES=cpu=4,mem=64190M,billing=4<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node06 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=4 CPULoad=0.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.6 NodeHostName=node06 Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=64190 AllocMem=0 FreeMem=63084 Sockets=4 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=4core <br> BootTime=2020-10-19T11:07:32 SlurmdStartTime=2020-10-19T11:07:51<br> CfgTRES=cpu=4,mem=64190M,billing=4<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node07 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=64 CPULoad=0.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.7 NodeHostName=node07 Version=20.02.3<br> OS=Linux 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 <br> RealMemory=80241 AllocMem=0 FreeMem=75316 Sockets=64 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=64core <br> BootTime=2020-10-13T20:52:40 SlurmdStartTime=2020-10-13T21:10:59<br> CfgTRES=cpu=64,mem=80241M,billing=64<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node08 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=64 CPULoad=0.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.8 NodeHostName=node08 Version=20.02.3<br> OS=Linux 3.10.0-514.el7.x86_64 #1 SMP Tue Nov 22 16:42:41 UTC 2016 <br> RealMemory=47987 AllocMem=0 FreeMem=42188 Sockets=64 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=64core <br> BootTime=2020-10-13T20:51:08 SlurmdStartTime=2020-10-13T20:57:12<br> CfgTRES=cpu=64,mem=47987M,billing=64<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node09 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=36 CPUTot=44 CPULoad=35.99<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.9 NodeHostName=node09 Version=20.02.3<br> OS=Linux 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC 2019 <br> RealMemory=128650 AllocMem=0 FreeMem=78059 Sockets=44 Boards=1<br> State=MIXED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=44core <br> BootTime=2020-10-13T20:47:11 SlurmdStartTime=2020-10-13T20:47:29<br> CfgTRES=cpu=44,mem=128650M,billing=44<br> AllocTRES=cpu=36<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node10 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=18 CPUTot=44 CPULoad=18.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.10 NodeHostName=node10 Version=20.02.3<br> OS=Linux 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC 2019 <br> RealMemory=128649 AllocMem=0 FreeMem=82279 Sockets=44 Boards=1<br> State=MIXED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=44core <br> BootTime=2020-10-13T20:47:36 SlurmdStartTime=2020-10-13T20:48:00<br> CfgTRES=cpu=44,mem=128649M,billing=44<br> AllocTRES=cpu=18<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node11 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=52 CPUTot=52 CPULoad=52.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.11 NodeHostName=node11 Version=20.02.3<br> OS=Linux 3.10.0-1127.13.1.el7.x86_64 #1 SMP Tue Jun 23 15:46:38 UTC 2020 <br> RealMemory=191932 AllocMem=0 FreeMem=147904 Sockets=52 Boards=1<br> State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=52core <br> BootTime=2020-10-13T20:47:02 SlurmdStartTime=2020-10-13T20:47:13<br> CfgTRES=cpu=52,mem=191932M,billing=52<br> AllocTRES=cpu=52<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node12 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=52 CPUTot=52 CPULoad=52.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.12 NodeHostName=node12 Version=20.02.3<br> OS=Linux 3.10.0-1127.13.1.el7.x86_64 #1 SMP Tue Jun 23 15:46:38 UTC 2020 <br> RealMemory=191932 AllocMem=0 FreeMem=162998 Sockets=52 Boards=1<br> State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=52core <br> BootTime=2020-10-13T20:47:31 SlurmdStartTime=2020-10-13T20:47:42<br> CfgTRES=cpu=52,mem=191932M,billing=52<br> AllocTRES=cpu=52<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br><br>NodeName=node13 Arch=x86_64 CoresPerSocket=1 <br> CPUAlloc=0 CPUTot=4 CPULoad=0.01<br> AvailableFeatures=(null)<br> ActiveFeatures=(null)<br> Gres=(null)<br> NodeAddr=10.0.0.13 NodeHostName=node13 Version=20.02.3<br> OS=Linux 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020 <br> RealMemory=31836 AllocMem=0 FreeMem=31093 Sockets=4 Boards=1<br> State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A<br> Partitions=4core <br> BootTime=2020-10-13T20:48:12 SlurmdStartTime=2020-10-13T20:48:20<br> CfgTRES=cpu=4,mem=31836M,billing=4<br> AllocTRES=<br> CapWatts=n/a<br> CurrentWatts=0 AveWatts=0<br> ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s<br> <br></div></div>
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