Something is not right. I think I misread your dayfile and in fast mkl threading is not active. Try something like env | grep -e MKL . I suspect that your job is just running on a single core.
On Thu, Oct 17, 2013 at 10:13 AM, Yundi Quan <quanyu...@gmail.com> wrote: > Sorry that I didn't make it clear. The dayfile was for cluster B. As I said > before, I always request one core per node and 8 nodes per job (number of k > points). I have 72 crystallographically non-equivalent atoms. > > On cluster B, I used the following R_LIB (LAPACK+BLAS) option to compile > WIEN2k. -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -iomp5 > > > Yundi > > > On Thu, Oct 17, 2013 at 7:50 AM, Laurence Marks <l-ma...@northwestern.edu> > wrote: >> >> I assume the dayfile was for cluster A, as wall is about 8x cpu which >> is about right for mkl multithreading which you are presumably using. >> You are not using mpi. You may want to compare the wall time to using >> on cluster A >> >> 1:node1:8 >> >> depending upon many factors it may be faster, or slower. This is only >> doing mpi using the bus not between nodes. >> >> Is it 72 unique atoms, or 72 total? >> >> My guess is that cluster A is about right. You can make it faster by >> using iterative diagonalization (-it or -it -noHinv) and perhaps >> reducing RKMAX -- you don't say what your RMTs are. >> >> For cluster B what blas/lapack are you using? Does it really have that >> many cores/node or is it using hyperthreading (which does not really >> give you much)? How is your NFS structured -- good communications or >> just slow ethernet? >> >> >> On Thu, Oct 17, 2013 at 9:33 AM, Yundi Quan <q...@ms.physics.ucdavis.edu> >> wrote: >> > Thanks for your reply. >> > a). both machines are set up in a way that once a node is assigned to a >> > job, >> > it cannot be assigned to another. >> > b). The .machines file looks like this >> > 1:node1 >> > 1:node2 >> > 1:node3 >> > 1:node4 >> > 1:node5 >> > 1:node6 >> > 1:node7 >> > 1:node8 >> > granularity:1 >> > extrafine:1 >> > lapw2_vector_split:1 >> > >> > I've been trying to avoid using mpi because sometime mpi can slow down >> > my >> > calculations because of poor communications between nodes. >> > >> > c). the amount of memory available to a core does not seem to be the >> > problem >> > in my case because my job could run smoothly on cluster A where each >> > node >> > has 8G memory and 8 core). But my job runs into memory problems on >> > cluster B >> > where each core has much more memory available. I wonder whether there >> > are >> > parameters which I should change in WIEN2k to reduce the memory usage. >> > >> > d). My dayfile for a single iteration looks like this. The wallclocks >> > are >> > around 500. >> > >> > >> > cycle 1 (Fri Oct 11 02:14:05 PDT 2013) (40/99 to go) >> > >> >> lapw0 -p (02:14:05) starting parallel lapw0 at Fri Oct 11 02:14:06 >> >> PDT >> >> 2013 >> > -------- .machine0 : processors >> > running lapw0 in single mode >> > 1431.414u 22.267s 24:14.84 99.9% 0+0k 0+0io 0pf+0w >> >> lapw1 -up -p -c (02:38:20) starting parallel lapw1 at Fri Oct 11 >> >> 02:38:20 PDT 2013 >> > -> starting parallel LAPW1 jobs at Fri Oct 11 02:38:21 PDT 2013 >> > running LAPW1 in parallel mode (using .machines) >> > 8 number_of_parallel_jobs >> > c1208-ib(1) 26558.265u 17.956s 7:34:14.39 97.5% 0+0k 0+0io 0pf+0w >> > c1201-ib(1) 26845.212u 15.496s 7:39:59.37 97.3% 0+0k 0+0io 0pf+0w >> > c1180-ib(1) 25872.609u 18.143s 7:23:53.43 97.2% 0+0k 0+0io 0pf+0w >> > c1179-ib(1) 26040.482u 17.868s 7:26:38.66 97.2% 0+0k 0+0io 0pf+0w >> > c1178-ib(1) 26571.271u 17.946s 7:34:16.23 97.5% 0+0k 0+0io 0pf+0w >> > c1177-ib(1) 27108.070u 34.294s 8:32:55.53 88.1% 0+0k 0+0io 0pf+0w >> > c1171-ib(1) 26729.399u 14.175s 7:36:22.67 97.6% 0+0k 0+0io 0pf+0w >> > c0844-ib(1) 25883.863u 47.148s 8:12:35.54 87.7% 0+0k 0+0io 0pf+0w >> > Summary of lapw1para: >> > c1208-ib k=1 user=26558.3 wallclock=454 >> > c1201-ib k=1 user=26845.2 wallclock=459 >> > c1180-ib k=1 user=25872.6 wallclock=443 >> > c1179-ib k=1 user=26040.5 wallclock=446 >> > c1178-ib k=1 user=26571.3 wallclock=454 >> > c1177-ib k=1 user=27108.1 wallclock=512 >> > c1171-ib k=1 user=26729.4 wallclock=456 >> > c0844-ib k=1 user=25883.9 wallclock=492 >> > 97.935u 34.265s 8:32:58.38 0.4% 0+0k 0+0io 0pf+0w >> >> lapw1 -dn -p -c (11:11:19) starting parallel lapw1 at Fri Oct 11 >> >> 11:11:19 PDT 2013 >> > -> starting parallel LAPW1 jobs at Fri Oct 11 11:11:19 PDT 2013 >> > running LAPW1 in parallel mode (using .machines.help) >> > 8 number_of_parallel_jobs >> > c1208-ib(1) 26474.686u 16.142s 7:33:36.01 97.3% 0+0k 0+0io 0pf+0w >> > c1201-ib(1) 26099.149u 40.330s 8:04:42.58 89.8% 0+0k 0+0io 0pf+0w >> > c1180-ib(1) 26809.287u 14.724s 7:38:56.52 97.4% 0+0k 0+0io 0pf+0w >> > c1179-ib(1) 26007.527u 17.959s 7:26:10.62 97.2% 0+0k 0+0io 0pf+0w >> > c1178-ib(1) 26565.723u 17.576s 7:35:20.11 97.3% 0+0k 0+0io 0pf+0w >> > c1177-ib(1) 27114.619u 31.180s 8:21:28.34 90.2% 0+0k 0+0io 0pf+0w >> > c1171-ib(1) 26474.665u 15.309s 7:33:38.15 97.3% 0+0k 0+0io 0pf+0w >> > c0844-ib(1) 26586.569u 15.010s 7:35:22.88 97.3% 0+0k 0+0io 0pf+0w >> > Summary of lapw1para: >> > c1208-ib k=1 user=26474.7 wallclock=453 >> > c1201-ib k=1 user=26099.1 wallclock=484 >> > c1180-ib k=1 user=26809.3 wallclock=458 >> > c1179-ib k=1 user=26007.5 wallclock=446 >> > c1178-ib k=1 user=26565.7 wallclock=455 >> > c1177-ib k=1 user=27114.6 wallclock=501 >> > c1171-ib k=1 user=26474.7 wallclock=453 >> > c0844-ib k=1 user=26586.6 wallclock=455 >> > 104.607u 18.798s 8:21:30.92 0.4% 0+0k 0+0io 0pf+0w >> >> lapw2 -up -p -c (19:32:50) running LAPW2 in parallel mode >> > c1208-ib 1016.517u 13.674s 17:11.10 99.9% 0+0k 0+0io 0pf+0w >> > c1201-ib 1017.359u 13.669s 17:11.82 99.9% 0+0k 0+0io 0pf+0w >> > c1180-ib 1033.056u 13.283s 17:27.07 99.9% 0+0k 0+0io 0pf+0w >> > c1179-ib 1037.551u 13.447s 17:31.50 99.9% 0+0k 0+0io 0pf+0w >> > c1178-ib 1019.156u 13.729s 17:13.49 99.9% 0+0k 0+0io 0pf+0w >> > c1177-ib 1021.878u 13.731s 17:16.07 99.9% 0+0k 0+0io 0pf+0w >> > c1171-ib 1032.417u 13.681s 17:26.70 99.9% 0+0k 0+0io 0pf+0w >> > c0844-ib 1022.315u 13.870s 17:16.81 99.9% 0+0k 0+0io 0pf+0w >> > Summary of lapw2para: >> > c1208-ib user=1016.52 wallclock=1031.1 >> > c1201-ib user=1017.36 wallclock=1031.82 >> > c1180-ib user=1033.06 wallclock=1047.07 >> > c1179-ib user=1037.55 wallclock=1051.5 >> > c1178-ib user=1019.16 wallclock=1033.49 >> > c1177-ib user=1021.88 wallclock=1036.07 >> > c1171-ib user=1032.42 wallclock=1046.7 >> > c0844-ib user=1022.32 wallclock=1036.81 >> > 31.923u 13.526s 18:20.12 4.1% 0+0k 0+0io 0pf+0w >> >> lapw2 -dn -p -c (19:51:10) running LAPW2 in parallel mode >> > c1208-ib 947.942u 13.364s 16:01.75 99.9% 0+0k 0+0io 0pf+0w >> > c1201-ib 932.766u 13.640s 15:49.22 99.7% 0+0k 0+0io 0pf+0w >> > c1180-ib 932.474u 13.609s 15:47.76 99.8% 0+0k 0+0io 0pf+0w >> > c1179-ib 936.171u 13.691s 15:50.33 99.9% 0+0k 0+0io 0pf+0w >> > c1178-ib 947.798u 13.493s 16:04.99 99.6% 0+0k 0+0io 0pf+0w >> > c1177-ib 947.786u 13.350s 16:04.89 99.6% 0+0k 0+0io 0pf+0w >> > c1171-ib 930.971u 13.874s 15:45.22 99.9% 0+0k 0+0io 0pf+0w >> > c0844-ib 950.723u 13.426s 16:04.69 99.9% 0+0k 0+0io 0pf+0w >> > Summary of lapw2para: >> > c1208-ib user=947.942 wallclock=961.75 >> > c1201-ib user=932.766 wallclock=949.22 >> > c1180-ib user=932.474 wallclock=947.76 >> > c1179-ib user=936.171 wallclock=950.33 >> > c1178-ib user=947.798 wallclock=964.99 >> > c1177-ib user=947.786 wallclock=964.89 >> > c1171-ib user=930.971 wallclock=945.22 >> > c0844-ib user=950.723 wallclock=964.69 >> > 31.522u 13.879s 16:53.13 4.4% 0+0k 0+0io 0pf+0w >> >> lcore -up (20:08:03) 2.993u 0.587s 0:03.75 95.2% 0+0k 0+0io 0pf+0w >> >> lcore -dn (20:08:07) 2.843u 0.687s 0:03.66 96.1% 0+0k 0+0io 0pf+0w >> >> mixer (20:08:21) 23.206u 32.513s 0:56.63 98.3% 0+0k 0+0io 0pf+0w >> > :ENERGY convergence: 0 0.00001 416.9302585700000000 >> > :CHARGE convergence: 0 0.0000 3.6278086 >> > >> > >> > On Thu, Oct 17, 2013 at 7:11 AM, Laurence Marks >> > <l-ma...@northwestern.edu> >> > wrote: >> >> >> >> There are so many possibilities, a few: >> >> >> >> a) If you only request 1 core/node most queuing systems (qsub/msub >> >> etc) will allocate the other cores to other jobs. You are then going >> >> to be very dependent upon what those other jobs are doing. Normal is >> >> to use all the cores on a given node. >> >> >> >> b) When you run on cluster B, in addition to a) it is going to be >> >> inefficient to run with mpi communications across nodes and it is much >> >> better to run on a given node across cores. Are you using a machines >> >> file with eight 1: nodeA lines (for instance) or one with a single 1: >> >> nodeA nodeB....? The first does not use mpi, the second does. To use >> >> mpi within a node you would use lines such as 1:node:8. Knowledge of >> >> your .machines file will help people assist you. >> >> >> >> c) The memory on those clusters is very small, whoever bought them was >> >> not thinking about large scale jobs. I look for at least 4G/core, and >> >> 2G/core is barely acceptable. You are going to have to use mpi. >> >> >> >> d) All mpi is equal, but some mpi is more equal than others. Depending >> >> upon whether you have infiniband, ethernet, openmpi, impi and how >> >> everything was compiled you can see enormous differences. One thing to >> >> look at is the difference between the cpu time and wall time (both in >> >> case.dayfile and at the bottom of case.output1_*). With a good mpi >> >> setup the wall time should be 5-10% more than the cpu time; with a bad >> >> setup it can be several times it. >> >> >> >> On Thu, Oct 17, 2013 at 8:44 AM, Yundi Quan <quanyu...@gmail.com> >> >> wrote: >> >> > Hi, >> >> > I have access to two clusters as a low-level user. One cluster >> >> > (cluster >> >> > A) >> >> > consists of nodes with 8 core and 8 G mem per node. The other cluster >> >> > (cluster B) has 24G mem per node and each node has 14 cores or more. >> >> > The >> >> > cores on cluster A are Xeon CPU E5620@2.40GHz, while the cores on >> >> > cluster B >> >> > are Xeon CPU X5550@2.67GH. From the specifications (2.40GHz+12288 KB >> >> > cache >> >> > vs 2.67GHz+8192 KB cache), two machines should be very close in >> >> > performance. >> >> > But it does not seem to be so. >> >> > >> >> > I have job with 72 atoms per unit cell. I initialized the job on >> >> > cluster >> >> > A >> >> > and ran it for a few iterations. Each iteration took 2 hours. Then, I >> >> > moved >> >> > the job to cluster B (14 cores per node with @2.67GHz). Now it takes >> >> > more >> >> > than 8 hours to finish one iteration. On both clusters, I request one >> >> > core >> >> > per node and 8 nodes per job ( 8 is the number of k points). I >> >> > compiled >> >> > WIEN2k_13 on cluster A without mpi. On cluster B, WIEN2k_12 was >> >> > compiled >> >> > by >> >> > the administrator with mpi. >> >> > >> >> > What could have caused poor performance of cluster B? Is it because >> >> > of >> >> > MPI? >> >> > >> >> > On an unrelated question. Sometimes memory would run out on cluster B >> >> > which >> >> > has 24Gmem per node. Nevertheless the same job could run smoothly on >> >> > cluster >> >> > A which only has 8 G per node. >> >> > >> >> > Thanks. >> >> >> >> >> >> >> >> -- >> >> Professor Laurence Marks >> >> Department of Materials Science and Engineering >> >> Northwestern University >> >> www.numis.northwestern.edu 1-847-491-3996 >> >> "Research is to see what everybody else has seen, and to think what >> >> nobody else has thought" >> >> Albert Szent-Gyorgi >> >> _______________________________________________ >> >> 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 >> > >> > >> >> >> >> -- >> Professor Laurence Marks >> Department of Materials Science and Engineering >> Northwestern University >> www.numis.northwestern.edu 1-847-491-3996 >> "Research is to see what everybody else has seen, and to think what >> nobody else has thought" >> Albert Szent-Gyorgi >> _______________________________________________ >> 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 > > -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi _______________________________________________ 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