[Wien] Intel(R) Xeon(R) CPU X5550 @ 2.67GHz vs Intel(R) Xeon(R) CPU E5620 @ 2.40GHz
Yundi Quan
quan at ms.physics.ucdavis.edu
Thu Oct 17 16:33:52 CEST 2013
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-marks at 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 <quanyundi at 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 at 2.40GHz, while the cores on
> cluster B
> > are Xeon CPU X5550 at 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 at 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20131017/6c5bb521/attachment.htm>
More information about the Wien
mailing list