29 May
2014
29 May
'14
2:41 p.m.
On 05/29/2014 02:21 PM, Kenneth Raffenetti wrote: > I do not [know where the source code to IBM's MPI > implementation on Blue Gene is]. RobL should know. I imagine you have to add it via softenv? Don't be shy, man! these messages should all be on the mpich-devel list, which I'm looping back in now. - you can add the mpich-ibm repository and then clone it with git. A bit of a mess, since V1R1M1 and V1R2M1 have a different directory structure. - you can browse the source on-line Mira is now (finally!) running V1R2M1, so follow the BGQ/IBM_V1R2M1/efix15 tag: http://git.mpich.org/mpich-ibm.git/tree/81ec186864f8cfe69ed9d99dfbd2d5ffd423e6cd:/mpich2 ==rob > > On 05/29/2014 02:15 PM, Junchao Zhang wrote: >> Ken, >> Do you know where is IBM MPI on mira? >> >> --Junchao Zhang >> >> >> ---------- Forwarded message ---------- >> From: *Thakur, Rajeev* <[email protected] <mailto:[email protected]>> >> Date: Thu, May 29, 2014 at 2:11 PM >> Subject: Re: [mpich-devel] MPI_Comm_Split/Dup scalability on BGQ and K >> supercomputers >> To: "Zhang, Junchao" <[email protected] <mailto:[email protected]>> >> Cc: "Balaji, Pavan" <[email protected] <mailto:[email protected]>> >> >> >> Can you look at the source code of IBM MPI on Mira to see what they are >> doing. I don't know if the source code is in our repo or somewhere else, >> but Rob Latham should know. >> >> Also, there is a bug in Comm_split in the latest version of MPI >> installed on Mira. There was a lot of discussion on the early-users >> mailing list. Rob Latham knows about it, and he can tell you what the >> bug is about. >> >> Rajeev >> >> >> On May 29, 2014, at 1:49 PM, Junchao Zhang <[email protected] >> <mailto:[email protected]>> >> wrote: >> >> > I did more experiments on Mira. But I feel I am lost :) In short, I >> think the original MPICH comm_split implementation is good if not the >> best. However, for unknown reasons, the MPI library provided by Mira >> is bad. >> > I wrote three micro-benchmarks, 1) qsort.c, which is a sequential C >> doe, to test the libc qsort performance when sorting a presorted array. >> 2) split.c, which measures MPI_Comm_split(MPI_COMM_WORLD, 0, myrank, >> ...). Note that all processes have the same color and use their old >> rank. The maximal time on processes is reported. 3) dup.c, which simply >> does MPI_Comm_dup(MPI_COMM_WORLD, &newcomm). >> > >> > I compiled the code using either mpixlc, which is provided by >> +mpiwrapper-gcc on Mira, or mpicc, which is built from mpich/master by >> myself, or mpicc-mergesort, which is also built by myself with a >> mergesort comm_split.c >> > >> > QSORT : compiled with mpixlc, run with 1 core on 1 node (also run >> with 16 cores simultaneously on 1 node, which gives even better >> results). The results indicate the libc-qsort used by mpixlc is good. >> > # integers time (s) >> > 64000 0.110789 >> > 125000 0.200747 >> > 512000 0.445075 >> > >> > COMM_SPLIT : compiled with mpixlc.(Note the results match with Sam's) >> > # ranks time (s) >> > 64000 2.297776 >> > 125000 8.157885 >> > 512000 237.079862 >> > >> > COMM_DUP : compiled with mpixlc (Note the results match with Sam's) >> > 64000 2.057966 >> > 125000 7.808858 >> > 512000 235.948144 >> > >> > COMM_SPLIT : compiled with mpicc, run two times. The variation is big >> at 512,000. >> > 64000 0.549024 0.545003 >> > 125000 0.959198 0.965059 >> > 512000 6.625385 3.716696 >> > >> > COMM_DUP : compiled with mpicc >> > 64000 0.028518 >> > 125000 0.056386 >> > 512000 0.202677 >> > >> > COMM_SPLIT : compiled with mpicc-mergesort >> > 64000 0.362572 >> > 125000 0.712167 >> > 512000 2.929134 >> > >> > COMM_DUP : compiled with mpicc-mergesort >> > 64000 0.028835 >> > 125000 0.055987 >> > 512000 0.202660 >> > >> > (Another difference should be mentioned is that mpixlc version is >> "MPICH2 version 1.5". I looked at the log history of comm_split.c. >> After MPICH2 1.5, there is no big changes) >> > We can see Comm_dup performance is independent of Comm_split and >> mpicc-mergesort is slightly better than mpicc. It may be still worth >> pushing mergesort to mpich. >> > >> > I have no idea why mpixlc is bad. Should I reported it to ALCF? >> > >> > --Junchao Zhang >> > >> > >> > On Wed, May 28, 2014 at 7:34 AM, Junchao Zhang <[email protected] >> <mailto:[email protected]>> wrote: >> > Fixed them. Thanks. >> > >> > --Junchao Zhang >> > >> > >> > On Tue, May 27, 2014 at 11:02 PM, Thakur, Rajeev <[email protected] >> <mailto:[email protected]>> wrote: >> > Junchao, >> > Your code looks fine, although I didn't check the merge >> sort in detail for potential bugs. You may want add a comment explaining >> that the 2x in the memory allocation for keytable is because the second >> half of it will be used as scratch space for the merge sort. Otherwise, >> someone looking at the code 3 years from now will miss it :-). Also, a >> typo in one comment: sortting -> sorting. >> > >> > Rajeev >> > >> > >> > On May 27, 2014, at 3:42 PM, Junchao Zhang <[email protected] >> <mailto:[email protected]>> wrote: >> > >> > > Here is the code. >> > > We do not just sort keys. We also want to keep track of old ranks >> for these keys. So we actually sort an array of {key, rank}. >> > > >> > > --Junchao Zhang >> > > >> > > >> > > On Tue, May 27, 2014 at 12:58 PM, Junchao Zhang >> <[email protected] <mailto:[email protected]>> wrote: >> > > Downloaded mpich2-1.3.1 and checked that . It uses bubble sort, >> which is a stable sort algorithm and no extra buffer is needed. >> > > merge sort is stable, but needs O(N) extra memory. I can allocate >> the array and the scratch together in one malloc instead of two mallocs >> separately. Let me do that. >> > > >> > > --Junchao Zhang >> > > >> > > >> > > On Tue, May 27, 2014 at 12:46 PM, Thakur, Rajeev >> <[email protected] <mailto:[email protected]>> wrote: >> > > The version I suggested (1.4) was not old enough. It has the new >> code with quick sort, not the old code with bubble sort. Instead, see >> 1.3.1 (http://www.mpich.org/static/downloads/1.3.1/). I confirmed that >> it has the old bubble sort. I believe it used O(p) less memory as well >> but I didn't recheck just now. >> > > >> > > Rajeev >> > > >> > > >> > > >> > > On May 27, 2014, at 12:38 PM, Junchao Zhang <[email protected] >> <mailto:[email protected]>> >> > > wrote: >> > > >> > > > I read the old code. It is not efficient. The code gathers {key, >> color (in effect it is later used to store old ranks) } and puts them in >> an array. Actually, that is enough info for a stable sort (i.e., using >> old ranks for ties). But the old code did not realize that and created >> a new type, splittype { key, color, orig_idx}, It assigns orig_idx the >> index of the element in array and uses that for ties. This is the O(p) >> memory you mentioned. We can say it adds 50% memory use. >> > > > For merge sort, the buffer has to be standalone (i.e., not mixed >> with old data). So I deleted the orig_idx field from splittype, and >> allocated a buffer as big as the original array, in effect adding 100% >> memory use. >> > > > I think we can have a fast qsort with 0% extra memory for our >> case. I will do that experiment later. >> > > > >> > > > --Junchao Zhang >> > > > >> > > > >> > > > On Tue, May 27, 2014 at 11:17 AM, Thakur, Rajeev >> <[email protected] <mailto:[email protected]>> wrote: >> > > > Junchao, >> > > > As far as I remember, when we switched from bubble >> sort to quicksort, we had to allocate additional O(nprocs) memory for >> the trick to make the qsort stable. You can check the old code in a >> release in 2011 (say 1.4 from >> http://www.mpich.org/static/downloads/1.4/). It would be good if we can >> avoid that additional memory allocation in the new sort. And if in the >> merge sort, you have added one more allocate, that should definitely be >> avoided. >> > > > >> > > > Rajeev >> > > > >> > > > >> > > > On May 27, 2014, at 9:40 AM, Junchao Zhang <[email protected] >> <mailto:[email protected]>> wrote: >> > > > >> > > > > Rejeev, >> > > > > The code is at mpich-review/commsplit. I pushed it there >> several days ago and MPICH test results look good. Could you review it? >> > > > > Yes, I will look why the improvement of Comm_dup is better. >> > > > > Another thing I want to investigate is: In Comm_split, we >> sort {key, old rank}, i.e., an integer pair. So basically, we have >> mechanisms to avoid the unstable problem of qsort. We can copy an >> optimized qsort instead of using the one in libc, and test its >> performance. The benefit of qsort is we can avoid the extra buffer >> needed in mergesort. Using a customized qsort, we can also avoid >> function pointer dereferencing. In libc qsort, one provides a generic >> comp function pointer. But our case is simple. We just want to compare >> integers. We can avoid the function call cost for each comparison. >> > > > > >> > > > > >> > > > > >> > > > > --Junchao Zhang >> > > > > >> > > > > >> > > > > On Tue, May 27, 2014 at 9:24 AM, Thakur, Rajeev >> <[email protected] <mailto:[email protected]>> wrote: >> > > > > Thanks. Have you run your new version through the MPICH test >> suite to make sure there are no bugs in the new sort. >> > > > > >> > > > > Can you look at Comm_dup to see why it improved so much. >> > > > > >> > > > > BG/Q has a relatively slower processor, so the sorting time is >> noticeable, unlike on the NERSC system. >> > > > > >> > > > > I think we should include it in 3.1.1 >> > > > > >> > > > > Rajeev >> > > > > >> > > > > On May 27, 2014, at 9:16 AM, Junchao Zhang <[email protected] >> <mailto:[email protected]>> >> > > > > wrote: >> > > > > >> > > > > > I tested Sam's HPGMG on Mira. I tried mpiwrapper-gcc and >> mpiwrapper-xl provided by the softenv of Mira, and also tried a >> self-built mpich with my own comm_split + mergesort. Here are test >> results. >> > > > > > >> > > > > > mpiwrapper-gcc and mpiwrapper-xl have similar results like >> the following (all time is in seconds) >> > > > > > # of ranks comm_dup comm_split MGBuild >> > > > > > 64000 2.059304 2.291601 28.085873 >> > > > > > 125000 7.807612 8.158366 88.644299 >> > > > > > 512000 235.923766 (no results due to job timed >> out) >> > > > > > >> > > > > > mpich-mergesort >> > > > > > # of ranks comm_dup comm_split MGBuild >> > > > > > 64000 0.046616 0.716383 6.999050 >> > > > > > 125000 0.065818 1.293382 10.696351 >> > > > > > 512000 0.229605 4.998839 52.467708 >> > > > > > >> > > > > > I don't know why the MPICH libraries on Mira are bad, since >> optimizations in qsort to avoid the worst case are not new. The libc >> library on Mira should have an optimized qsort. >> > > > > > Another thing I have not looked into is why comm_dup is >> affected by comm_split. It seems comm_dup calls comm_split internally. >> > > > > > >> > > > > > In short, the current mergesort solution largely fixes the >> scaling problem. We may further investigate the issue and come up with >> better solutions. But if you think this is a key fix, probably we can >> push it to 3.1.1. >> > > > > > >> > > > > > >> > > > > > --Junchao Zhang >> > > > > > >> > > > > > >> > > > > > On Sun, May 25, 2014 at 12:25 PM, Junchao Zhang >> <[email protected] <mailto:[email protected]>> wrote: >> > > > > > Yes, I am going to test that. >> > > > > > >> > > > > > --Junchao Zhang >> > > > > > >> > > > > > >> > > > > > On Sun, May 25, 2014 at 11:11 AM, Thakur, Rajeev >> <[email protected] <mailto:[email protected]>> wrote: >> > > > > > Can you also see if the xlc compiler makes any difference? >> > > > > > >> > > > > > Rajeev >> > > > > > >> > > > > > On May 25, 2014, at 8:14 AM, Junchao Zhang >> <[email protected] <mailto:[email protected]>> >> > > > > > wrote: >> > > > > > >> > > > > > > I tested hpgmg on Mira and reproduced the scaling problem. >> I used mpiwrapper-gcc. >> > > > > > > With 64000 MPI tasks, the output is: >> > > > > > > Duplicating MPI_COMM_WORLD...done (2.059304 seconds) >> > > > > > > Building MPI subcommunicators..., level 1...done (2.291601 >> seconds) >> > > > > > > Total time in MGBuild 28.085873 seconds >> > > > > > > With 125000 MPI Tasks, the output is: >> > > > > > > Duplicating MPI_COMM_WORLD...done (7.807612 seconds) >> > > > > > > Building MPI subcommunicators..., level 1...done (8.158366 >> seconds) >> > > > > > > Total time in MGBuild 88.644299 seconds >> > > > > > > >> > > > > > > Let me replace qsort with mergesort in Comm_split to see >> what will happen. >> > > > > > > >> > > > > > > --Junchao Zhang >> > > > > > > >> > > > > > > >> > > > > > > On Sat, May 24, 2014 at 9:07 AM, Sam Williams >> <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > I saw the problem on Mira and K but not Edison. I don't >> know if that is due to scale or implementation. >> > > > > > > >> > > > > > > On Mira, I was running jobs with a 10min wallclock limit. >> I scaled to 46656 processes with 64 threads per process (c1, >> OMP_NUM_THREADS=64) and all jobs completed successfully. However, I was >> only looking at MGSolve times and not MGBuild times. I then decided to >> explore 8 threads per process (c8, OMP_NUM_THREADS=8) and started at the >> high concurrency. The jobs timed out while still in MGBuild after >> 10mins with 373248 processes as well as with a 20min timeout. At that >> point I added the USE_SUBCOMM option to enable/disable the use of >> comm_split. I haven't tried scaling with the sub communicator on Mira >> since then. >> > > > > > > >> > > > > > > >> > > > > > > On May 24, 2014, at 6:39 AM, Junchao Zhang >> <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > >> > > > > > > > Hi, Sam, >> > > > > > > > Could you give me the exact number of MPI ranks for >> your results on Mira? >> > > > > > > > I run hpgmg on Edison with export OMP_NUM_THREADS=1, >> aprun -n 64000 -ss -cc numa_node ./hpgmg-fv 6 1. The total time in >> MGBuild is about 0.005 seconds. I was wondering how many cores I need to >> apply to reproduce the problem. >> > > > > > > > Thanks. >> > > > > > > > >> > > > > > > > >> > > > > > > > --Junchao Zhang >> > > > > > > > >> > > > > > > > >> > > > > > > > On Sat, May 17, 2014 at 9:06 AM, Sam Williams >> <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > > I've been conducting scaling experiments on the Mira >> (Blue Gene/Q) and K (Sparc) supercomputers. I've noticed that the time >> required for MPI_Comm_split and MPI_Comm_dup can grow quickly with scale >> (~P^2). As such, its performance eventually becomes a bottleneck. That >> is, although the benefit of using a subcommunicator is huge (multigrid >> solves are weak-scalable), the penalty of creating one (multigrid build >> time) is also huge. >> > > > > > > > >> > > > > > > > For example, when scaling from 1 to 46K nodes (= cubes of >> integers) on Mira, the time (in seconds) required to build a MG solver >> (including a subcommunicator) scales as >> > > > > > > > 222335.output: Total time in MGBuild 0.056704 >> > > > > > > > 222336.output: Total time in MGBuild 0.060834 >> > > > > > > > 222348.output: Total time in MGBuild 0.064782 >> > > > > > > > 222349.output: Total time in MGBuild 0.090229 >> > > > > > > > 222350.output: Total time in MGBuild 0.075280 >> > > > > > > > 222351.output: Total time in MGBuild 0.091852 >> > > > > > > > 222352.output: Total time in MGBuild 0.137299 >> > > > > > > > 222411.output: Total time in MGBuild 0.301552 >> > > > > > > > 222413.output: Total time in MGBuild 0.606444 >> > > > > > > > 222415.output: Total time in MGBuild 0.745272 >> > > > > > > > 222417.output: Total time in MGBuild 0.779757 >> > > > > > > > 222418.output: Total time in MGBuild 4.671838 >> > > > > > > > 222419.output: Total time in MGBuild 15.123162 >> > > > > > > > 222420.output: Total time in MGBuild 33.875626 >> > > > > > > > 222421.output: Total time in MGBuild 49.494547 >> > > > > > > > 222422.output: Total time in MGBuild 151.329026 >> > > > > > > > >> > > > > > > > If I disable the call to MPI_Comm_Split, my time scales as >> > > > > > > > 224982.output: Total time in MGBuild 0.050143 >> > > > > > > > 224983.output: Total time in MGBuild 0.052607 >> > > > > > > > 224988.output: Total time in MGBuild 0.050697 >> > > > > > > > 224989.output: Total time in MGBuild 0.078343 >> > > > > > > > 224990.output: Total time in MGBuild 0.054634 >> > > > > > > > 224991.output: Total time in MGBuild 0.052158 >> > > > > > > > 224992.output: Total time in MGBuild 0.060286 >> > > > > > > > 225008.output: Total time in MGBuild 0.062925 >> > > > > > > > 225009.output: Total time in MGBuild 0.097357 >> > > > > > > > 225010.output: Total time in MGBuild 0.061807 >> > > > > > > > 225011.output: Total time in MGBuild 0.076617 >> > > > > > > > 225012.output: Total time in MGBuild 0.099683 >> > > > > > > > 225013.output: Total time in MGBuild 0.125580 >> > > > > > > > 225014.output: Total time in MGBuild 0.190711 >> > > > > > > > 225016.output: Total time in MGBuild 0.218329 >> > > > > > > > 225017.output: Total time in MGBuild 0.282081 >> > > > > > > > >> > > > > > > > Although I didn't directly measure it, this suggests the >> time for MPI_Comm_Split is growing roughly quadratically with process >> concurrency. >> > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > I see the same effect on the K machine (8...64K nodes) >> where the code uses comm_split/dup in conjunction: >> > > > > > > > run00008_7_1.sh.o2412931: Total time in MGBuild >> 0.026458 seconds >> > > > > > > > run00064_7_1.sh.o2415876: Total time in MGBuild >> 0.039121 seconds >> > > > > > > > run00512_7_1.sh.o2415877: Total time in MGBuild >> 0.086800 seconds >> > > > > > > > run01000_7_1.sh.o2414496: Total time in MGBuild >> 0.129764 seconds >> > > > > > > > run01728_7_1.sh.o2415878: Total time in MGBuild >> 0.224576 seconds >> > > > > > > > run04096_7_1.sh.o2415880: Total time in MGBuild >> 0.738979 seconds >> > > > > > > > run08000_7_1.sh.o2414504: Total time in MGBuild >> 2.123800 seconds >> > > > > > > > run13824_7_1.sh.o2415881: Total time in MGBuild >> 6.276573 seconds >> > > > > > > > run21952_7_1.sh.o2415882: Total time in MGBuild >> 13.634200 seconds >> > > > > > > > run32768_7_1.sh.o2415884: Total time in MGBuild >> 36.508670 seconds >> > > > > > > > run46656_7_1.sh.o2415874: Total time in MGBuild >> 58.668228 seconds >> > > > > > > > run64000_7_1.sh.o2415875: Total time in MGBuild >> 117.322217 seconds >> > > > > > > > >> > > > > > > > >> > > > > > > > A glance at the implementation on Mira (I don't know if >> the implementation on K is stock) suggests it should be using qsort to >> sort based on keys. Unfortunately, qsort is not performance robust like >> heap/merge sort. If one were to be productive and call comm_split >> like... >> > > > > > > > MPI_Comm_split(...,mycolor,myrank,...) >> > > > > > > > then one runs the risk that the keys are presorted. This >> hits the worst case computational complexity for qsort... O(P^2). >> Demanding programmers avoid sending sorted keys seems unreasonable. >> > > > > > > > >> > > > > > > > >> > > > > > > > I should note, I see a similar lack of scaling with >> MPI_Comm_dup on the K machine. Unfortunately, my BGQ data used an >> earlier version of the code that did not use comm_dup. As such, I can’t >> definitively say that it is a problem on that machine as well. >> > > > > > > > >> > > > > > > > Thus, I'm asking for scalable implementations of >> comm_split/dup using merge/heap sort whose worst case complexity is >> still PlogP to be prioritized in the next update. >> > > > > > > > >> > > > > > > > >> > > > > > > > thanks >> > > > > > > > _______________________________________________ >> > > > > > > > To manage subscription options or unsubscribe: >> > > > > > > > https://lists.mpich.org/mailman/listinfo/devel >> > > > > > > > >> > > > > > > > _______________________________________________ >> > > > > > > > To manage subscription options or unsubscribe: >> > > > > > > > https://lists.mpich.org/mailman/listinfo/devel >> > > > > > > >> > > > > > > _______________________________________________ >> > > > > > > To manage subscription options or unsubscribe: >> > > > > > > https://lists.mpich.org/mailman/listinfo/devel >> > > > > > > >> > > > > > > _______________________________________________ >> > > > > > > To manage subscription options or unsubscribe: >> > > > > > > https://lists.mpich.org/mailman/listinfo/devel >> > > > > > >> > > > > > >> > > > > > >> > > > > >> > > > > >> > > > >> > > > >> > > >> > > >> > > >> > > <comm_split.c> >> > >> > >> > >> >> -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA