Memory should be fine since I have chosen an idle node to do the tests and I have tested a few omp_global values, it still performed badly. So, it should be a file/network issue as Prof. Blaha suggested since I have indeed set the SCRATCH directory as ./. Anyway, thank you for your suggestions.
Laurence Marks <laurence.ma...@gmail.com> 于2020年12月28日周一 下午7:13写道: > While the server is probably the issue, two other things to check: > a) lapw2 can need more memory, so swapping issues are not impossible. > b) How have you set omp_lapw2 ? > > _____ > Professor Laurence Marks > "Research is to see what everybody else has seen, and to think what nobody > else has thought", Albert Szent-Gyorgi > www.numis.northwestern.edu > > On Mon, Dec 28, 2020, 03:23 Fan <fxinwei...@gmail.com> wrote: > >> Thank you for your quick response. I believe that is the key to the >> problem. So with larger vector files, the lapw2 will run slower in my >> situation. That makes sense. >> >> Peter Blaha <pbl...@theochem.tuwien.ac.at> 于2020年12月28日周一 下午4:38写道: >> >>> This points to a fileserver/network problem on your cluster. >>> >>> On a big cluster one usually has a home-directory on a fileserver drive, >>> which is mounted over a network (eg. NFS, HPFS,..) on all nodes. While >>> this is very convenient, it is on many systems also a huge bottleneck. >>> Either the fileserver breaks down due to too many simultaneously >>> requests or the network does not have sufficient band width. >>> >>> You probably have set the SCRATCH variable to your working directory >>> "./", which means that the large case.vector* files are stored in your >>> working directory, leading to the bad performance of lapw2. >>> >>> On most clusters there is a local scratch or tmp directory (files exist >>> only on this node) and when setting your SCRATCH variable to this, the >>> slow lapw2 should be gone. >>> >>> In addition, I see that also lapw1 gets only 90% of a core. I recommend >>> setting OMP_NUM_THREADS=2 and spanning only 4 k-parallel jobs in >>> parallel (I assume you have a node with 8 cores). >>> >>> >>> On 12/28/20 9:14 AM, Fan wrote: >>> > Dear wien2k users, >>> > >>> > I am trying to run wien2k on clusters, but I encountered a very >>> strange >>> > issue that the performance of lapw2 is very inefficient. For example, >>> > >>> > >>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------- >>> > > lapw1 -dn -p (15:27:45) starting parallel lapw1 at Mon Dec >>> > 28 15:27:46 CST 2020 >>> > -> starting parallel LAPW1 jobs at Mon Dec 28 15:27:46 CST 2020 >>> > running LAPW1 in parallel mode (using .machines.help) >>> > 8 number_of_parallel_jobs >>> > f02n10(58) 178.212u 3.134s 3:15.91 92.57% 0+0k 0+0io 0pf+0w >>> > f02n10(58) 180.210u 3.011s 3:19.46 91.86% 0+0k 0+0io 0pf+0w >>> > f02n10(58) 183.239u 3.019s 3:22.73 91.87% 0+0k 0+0io 0pf+0w >>> > f02n10(57) 181.113u 2.884s 3:20.20 91.90% 0+0k 0+0io 0pf+0w >>> > f02n10(57) 178.433u 2.965s 3:18.85 91.22% 0+0k 0+0io 0pf+0w >>> > f02n10(57) 151.420u 2.756s 2:48.26 91.63% 0+0k 0+0io 0pf+0w >>> > f02n10(57) 183.799u 3.065s 3:22.58 92.24% 0+0k 0+0io 0pf+0w >>> > f02n10(57) 185.867u 3.109s 3:27.50 91.07% 0+0k 0+0io 0pf+0w >>> > Summary of lapw1para: >>> > f02n10 k=459 user=1422.29 wallclock=1575.49 >>> > 1.034u 1.698s 3:30.15 1.2% 0+0k 472+128io 2pf+0w >>> > > lapw2 -up -p (15:31:16) running LAPW2 in parallel mode >>> > f02n10 37.680u 1.597s 6:32.94 10.00% 0+0k 0+0io 0pf+0w >>> > f02n10 38.841u 1.682s 7:07.57 9.48% 0+0k 0+0io 0pf+0w >>> > f02n10 38.611u 1.727s 6:51.53 9.80% 0+0k 0+0io 0pf+0w >>> > f02n10 38.715u 1.728s 6:48.76 9.89% 0+0k 0+0io 0pf+0w >>> > f02n10 37.847u 1.639s 7:01.08 9.38% 0+0k 0+0io 0pf+0w >>> > f02n10 38.170u 1.709s 6:45.01 9.85% 0+0k 0+0io 0pf+0w >>> > f02n10 39.261u 1.727s 7:01.11 9.73% 0+0k 0+0io 0pf+0w >>> > f02n10 39.772u 1.765s 7:04.40 9.79% 0+0k 0+0io 0pf+0w >>> > >>> > >>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------- >>> > As you can see the cpu utilizations are much lower than that of lapw1, >>> > which made lawp2 more time-consuming than lapw1. MPI parallelization >>> > performed even worse. >>> > >>> > More strangely, it seems to be case-dependent. For TiC and some other >>> > systems, it works fine. I also tried other nodes, the problem still >>> > persists, however in my local workstation everything went well. >>> > >>> > The version of wien2k is 19.2 compiled with intel icc and ifort >>> without >>> > any errors. MPI, FFTW, and ELPA are all available. >>> > >>> > Any suggestion will be appreciated. >>> > >>> > Fan >>> > >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Wien mailing list >>> > Wien@zeus.theochem.tuwien.ac.at >>> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >>> <https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0O2-yJfew$> >>> > SEARCH the MAILING-LIST at: >>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >>> <https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0OxfQ5bgA$> >>> > >>> >>> -- >>> >>> P.Blaha >>> >>> -------------------------------------------------------------------------- >>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna >>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 >>> Email: bl...@theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at >>> <https://urldefense.com/v3/__http://www.wien2k.at__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0NUbjv7Xw$> >>> WWW: http://www.imc.tuwien.ac.at/TC_Blaha >>> <https://urldefense.com/v3/__http://www.imc.tuwien.ac.at/TC_Blaha__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0PkvhVHaQ$> >>> >>> -------------------------------------------------------------------------- >>> _______________________________________________ >>> Wien mailing list >>> Wien@zeus.theochem.tuwien.ac.at >>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >>> <https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0O2-yJfew$> >>> SEARCH the MAILING-LIST at: >>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >>> <https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0OxfQ5bgA$> >>> >> _______________________________________________ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> >> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0O2-yJfew$ >> SEARCH the MAILING-LIST at: >> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!EjV3JB-TAlZJGOYIcsqasIMWKmgqDXUbL1tizifidFHUioB3wf4Tl84i7MNpF0OxfQ5bgA$ >> > _______________________________________________ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >
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