Hi all We have been using OpenMPI for many years with Ubuntu on our 20-node cluster. Each node has 2 quad cores, so we usually run up to 8 processes on each node up to a maximum of 160 processes.
However, we just upgraded the cluster to Ubuntu 11.04 with Open MPI 1.4.3 and and have come across a strange behavior where mpi programs run perfectly well when confined to one node but hangs during communication across multiple nodes. We have no idea why and would like some help in debugging this. A small MPI test program is attached and typical output shown below. Hope someone can help us Cheers and thanks Ole Nielsen -------------------- Test output across two nodes (This one hangs) -------------------------- nielso@alamba:~/sandpit/pypar/source$ mpirun --hostfile /etc/mpihosts --host node17,node18 --npernode 2 a.out Number of processes = 4 Test repeated 3 times for reliability I am process 1 on node node17 P1: Waiting to receive from to P0 I am process 0 on node node17 Run 1 of 3 P0: Sending to P1 I am process 2 on node node18 P2: Waiting to receive from to P1 I am process 3 on node node18 P3: Waiting to receive from to P2 P1: Sending to to P2 -------------------- Test output within one node (This one is OK) -------------------------- nielso@alamba:~/sandpit/pypar/source$ mpirun --hostfile /etc/mpihosts --host node17 --npernode 4 a.out Number of processes = 4 Test repeated 3 times for reliability I am process 2 on node node17 P2: Waiting to receive from to P1 I am process 0 on node node17 Run 1 of 3 P0: Sending to P1 I am process 1 on node node17 P1: Waiting to receive from to P0 I am process 3 on node node17 P3: Waiting to receive from to P2 P1: Sending to to P2 P2: Sending to to P3 P1: Waiting to receive from to P0 P2: Waiting to receive from to P1 P3: Sending to to P0 P0: Received from to P3 Run 2 of 3 P0: Sending to P1 P3: Waiting to receive from to P2 P1: Sending to to P2 P2: Sending to to P3 P1: Waiting to receive from to P0 P3: Sending to to P0 P2: Waiting to receive from to P1 P0: Received from to P3 Run 3 of 3 P0: Sending to P1 P3: Waiting to receive from to P2 P1: Sending to to P2 P2: Sending to to P3 P1: Done P2: Done P3: Sending to to P0 P0: Received from to P3 P0: Done P3: Done
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><td><span title="Add comment" onclick="codereviews.startEdit('svn98',75);"> </span ></td><td id="75"><a href="#75">75</a></td></tr ><tr id="gr_svn98_76" onmouseover="gutterOver(76)" ><td><span title="Add comment" onclick="codereviews.startEdit('svn98',76);"> </span ></td><td id="76"><a href="#76">76</a></td></tr ><tr id="gr_svn98_77" onmouseover="gutterOver(77)" ><td><span title="Add comment" onclick="codereviews.startEdit('svn98',77);"> </span ></td><td id="77"><a href="#77">77</a></td></tr ><tr id="gr_svn98_78" onmouseover="gutterOver(78)" ><td><span title="Add comment" onclick="codereviews.startEdit('svn98',78);"> </span ></td><td id="78"><a href="#78">78</a></td></tr ></table></pre> <pre><table width="100%"><tr class="nocursor"><td></td></tr></table></pre> </td> <td id="lines"> <pre><table width="100%"><tr class="cursor_stop cursor_hidden"><td></td></tr></table></pre> <pre class="prettyprint lang-c"><table id="src_table_0"><tr id=sl_svn98_1 onmouseover="gutterOver(1)" ><td class="source">/*<br></td></tr ><tr id=sl_svn98_2 onmouseover="gutterOver(2)" ><td class="source"> Simple MPI communication test.<br></td></tr ><tr id=sl_svn98_3 onmouseover="gutterOver(3)" ><td class="source"> Ole Moller Nielsen - 2011<br></td></tr ><tr id=sl_svn98_4 onmouseover="gutterOver(4)" ><td class="source">*/<br></td></tr ><tr id=sl_svn98_5 onmouseover="gutterOver(5)" ><td class="source"><br></td></tr ><tr id=sl_svn98_6 onmouseover="gutterOver(6)" ><td class="source">#include <stdio.h><br></td></tr ><tr id=sl_svn98_7 onmouseover="gutterOver(7)" ><td class="source">#include <stdlib.h><br></td></tr ><tr id=sl_svn98_8 onmouseover="gutterOver(8)" ><td class="source">#include <mpi.h><br></td></tr ><tr id=sl_svn98_9 onmouseover="gutterOver(9)" ><td class="source"><br></td></tr ><tr id=sl_svn98_10 onmouseover="gutterOver(10)" ><td class="source"><br></td></tr ><tr id=sl_svn98_11 onmouseover="gutterOver(11)" ><td class="source">#define M 500000 /* Data size */<br></td></tr ><tr id=sl_svn98_12 onmouseover="gutterOver(12)" ><td class="source"><br></td></tr ><tr id=sl_svn98_13 onmouseover="gutterOver(13)" ><td class="source"><br></td></tr ><tr id=sl_svn98_14 onmouseover="gutterOver(14)" ><td class="source">int main(int argc, char **argv) {<br></td></tr ><tr id=sl_svn98_15 onmouseover="gutterOver(15)" ><td class="source"> int repeats = 3, msgid = 0;<br></td></tr ><tr id=sl_svn98_16 onmouseover="gutterOver(16)" ><td class="source"> int myid, procs;<br></td></tr ><tr id=sl_svn98_17 onmouseover="gutterOver(17)" ><td class="source"> int j, k;<br></td></tr ><tr id=sl_svn98_18 onmouseover="gutterOver(18)" ><td class="source"><br></td></tr ><tr id=sl_svn98_19 onmouseover="gutterOver(19)" ><td class="source"> double A[M];<br></td></tr ><tr id=sl_svn98_20 onmouseover="gutterOver(20)" ><td class="source"><br></td></tr ><tr id=sl_svn98_21 onmouseover="gutterOver(21)" ><td class="source"> int namelen;<br></td></tr ><tr id=sl_svn98_22 onmouseover="gutterOver(22)" ><td class="source"> char processor_name[MPI_MAX_PROCESSOR_NAME];<br></td></tr ><tr id=sl_svn98_23 onmouseover="gutterOver(23)" ><td class="source"><br></td></tr ><tr id=sl_svn98_24 onmouseover="gutterOver(24)" ><td class="source"> MPI_Status stat;<br></td></tr ><tr id=sl_svn98_25 onmouseover="gutterOver(25)" ><td class="source"><br></td></tr ><tr id=sl_svn98_26 onmouseover="gutterOver(26)" ><td class="source"><br></td></tr ><tr id=sl_svn98_27 onmouseover="gutterOver(27)" ><td class="source"> /* Initialize */<br></td></tr ><tr id=sl_svn98_28 onmouseover="gutterOver(28)" ><td class="source"> MPI_Init(&argc, &argv);<br></td></tr ><tr id=sl_svn98_29 onmouseover="gutterOver(29)" ><td class="source"> MPI_Comm_size(MPI_COMM_WORLD, &procs);<br></td></tr ><tr id=sl_svn98_30 onmouseover="gutterOver(30)" ><td class="source"> MPI_Comm_rank(MPI_COMM_WORLD, &myid);<br></td></tr ><tr id=sl_svn98_31 onmouseover="gutterOver(31)" ><td class="source"> MPI_Get_processor_name(processor_name, &namelen);<br></td></tr ><tr id=sl_svn98_32 onmouseover="gutterOver(32)" ><td class="source"><br></td></tr ><tr id=sl_svn98_33 onmouseover="gutterOver(33)" ><td class="source"> if (myid == 0) {<br></td></tr ><tr id=sl_svn98_34 onmouseover="gutterOver(34)" ><td class="source"> printf("Number of processes = %d\n", procs);<br></td></tr ><tr id=sl_svn98_35 onmouseover="gutterOver(35)" ><td class="source"> printf("Test repeated %d times for reliability\n", repeats);<br></td></tr ><tr id=sl_svn98_36 onmouseover="gutterOver(36)" ><td class="source"> }<br></td></tr ><tr id=sl_svn98_37 onmouseover="gutterOver(37)" ><td class="source"><br></td></tr ><tr id=sl_svn98_38 onmouseover="gutterOver(38)" ><td class="source"> if (procs < 2) {<br></td></tr ><tr id=sl_svn98_39 onmouseover="gutterOver(39)" ><td class="source"> printf("Program needs at least two processors - aborting\n");<br></td></tr ><tr id=sl_svn98_40 onmouseover="gutterOver(40)" ><td class="source"> MPI_Abort(MPI_COMM_WORLD,999);<br></td></tr ><tr id=sl_svn98_41 onmouseover="gutterOver(41)" ><td class="source"> }<br></td></tr ><tr id=sl_svn98_42 onmouseover="gutterOver(42)" ><td class="source"><br></td></tr ><tr id=sl_svn98_43 onmouseover="gutterOver(43)" ><td class="source"> /* Create the data */<br></td></tr ><tr id=sl_svn98_44 onmouseover="gutterOver(44)" ><td class="source"> for (j=0; j<M; j++) {<br></td></tr ><tr id=sl_svn98_45 onmouseover="gutterOver(45)" ><td class="source"> A[j]=rand();<br></td></tr ><tr id=sl_svn98_46 onmouseover="gutterOver(46)" ><td class="source"> }<br></td></tr ><tr id=sl_svn98_47 onmouseover="gutterOver(47)" ><td class="source"><br></td></tr ><tr id=sl_svn98_48 onmouseover="gutterOver(48)" ><td class="source"> /* Synchronize */<br></td></tr ><tr id=sl_svn98_49 onmouseover="gutterOver(49)" ><td class="source"> MPI_Barrier(MPI_COMM_WORLD);<br></td></tr ><tr id=sl_svn98_50 onmouseover="gutterOver(50)" ><td class="source"> printf("I am process %d on node %s\n", myid, processor_name);<br></td></tr ><tr id=sl_svn98_51 onmouseover="gutterOver(51)" ><td class="source"><br></td></tr ><tr id=sl_svn98_52 onmouseover="gutterOver(52)" ><td class="source"> /* Pass msg circularly a number of times*/<br></td></tr ><tr id=sl_svn98_53 onmouseover="gutterOver(53)" ><td class="source"> for (k=0; k<repeats; k++) {<br></td></tr ><tr id=sl_svn98_54 onmouseover="gutterOver(54)" ><td class="source"> if (myid == 0) {<br></td></tr ><tr id=sl_svn98_55 onmouseover="gutterOver(55)" ><td class="source"> printf("Run %d of %d\n", k+1, repeats);<br></td></tr ><tr id=sl_svn98_56 onmouseover="gutterOver(56)" ><td class="source"> }<br></td></tr ><tr id=sl_svn98_57 onmouseover="gutterOver(57)" ><td class="source"><br></td></tr ><tr id=sl_svn98_58 onmouseover="gutterOver(58)" ><td class="source"> /* Communicate*/<br></td></tr ><tr id=sl_svn98_59 onmouseover="gutterOver(59)" ><td class="source"> if (myid == 0) {<br></td></tr ><tr id=sl_svn98_60 onmouseover="gutterOver(60)" ><td class="source"> printf("P%i: Sending to P%i\n", myid, 1);<br></td></tr ><tr id=sl_svn98_61 onmouseover="gutterOver(61)" ><td class="source"> MPI_Send(&A[0], M, MPI_DOUBLE, 1, msgid, MPI_COMM_WORLD);<br></td></tr ><tr id=sl_svn98_62 onmouseover="gutterOver(62)" ><td class="source"> MPI_Recv(&A[0], M, MPI_DOUBLE, procs-1, msgid, MPI_COMM_WORLD, &stat);<br></td></tr ><tr id=sl_svn98_63 onmouseover="gutterOver(63)" ><td class="source"> printf("P%i: Received from to P%i\n", myid, procs-1);<br></td></tr ><tr id=sl_svn98_64 onmouseover="gutterOver(64)" ><td class="source"> } else {<br></td></tr ><tr id=sl_svn98_65 onmouseover="gutterOver(65)" ><td class="source"> printf("P%i: Waiting to receive from to P%i\n", myid, myid-1);<br></td></tr ><tr id=sl_svn98_66 onmouseover="gutterOver(66)" ><td class="source"> MPI_Recv(&A[0], M, MPI_DOUBLE, myid-1, msgid, MPI_COMM_WORLD, &stat);<br></td></tr ><tr id=sl_svn98_67 onmouseover="gutterOver(67)" ><td class="source"> printf("P%i: Sending to to P%i\n", myid, (myid+1)%procs);<br></td></tr ><tr id=sl_svn98_68 onmouseover="gutterOver(68)" ><td class="source"> MPI_Send(&A[0], M, MPI_DOUBLE, (myid+1)%procs, msgid, MPI_COMM_WORLD);<br></td></tr ><tr id=sl_svn98_69 onmouseover="gutterOver(69)" ><td class="source"> }<br></td></tr ><tr id=sl_svn98_70 onmouseover="gutterOver(70)" ><td class="source"> }<br></td></tr ><tr id=sl_svn98_71 onmouseover="gutterOver(71)" ><td class="source"><br></td></tr ><tr id=sl_svn98_72 onmouseover="gutterOver(72)" ><td class="source"><br></td></tr ><tr id=sl_svn98_73 onmouseover="gutterOver(73)" ><td class="source"> printf("P%i: Done\n", myid);<br></td></tr ><tr id=sl_svn98_74 onmouseover="gutterOver(74)" ><td class="source"><br></td></tr ><tr id=sl_svn98_75 onmouseover="gutterOver(75)" ><td class="source"> MPI_Finalize();<br></td></tr ><tr id=sl_svn98_76 onmouseover="gutterOver(76)" ><td class="source"> return 0;<br></td></tr ><tr id=sl_svn98_77 onmouseover="gutterOver(77)" ><td class="source">}<br></td></tr ><tr id=sl_svn98_78 onmouseover="gutterOver(78)" ><td class="source"><br></td></tr ></table></pre> <pre><table width="100%"><tr class="cursor_stop cursor_hidden"><td></td></tr></table></pre> </td> </tr></table> <script type="text/javascript"> var lineNumUnderMouse = -1; function gutterOver(num) { gutterOut(); var newTR = document.getElementById('gr_svn98_' + num); if (newTR) { newTR.className = 'undermouse'; } lineNumUnderMouse = num; } function gutterOut() { if (lineNumUnderMouse != -1) { var oldTR = document.getElementById( 'gr_svn98_' + lineNumUnderMouse); if (oldTR) { oldTR.className = ''; } lineNumUnderMouse = -1; } } var numsGenState = {table_base_id: 'nums_table_'}; var srcGenState = {table_base_id: 'src_table_'}; var alignerRunning = false; var startOver = false; function setLineNumberHeights() { if (alignerRunning) { startOver = true; return; } numsGenState.chunk_id = 0; numsGenState.table = document.getElementById('nums_table_0'); 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kibbles.keys.addKeyPressListener( 'u', function() { window.location = detail_url; }); kibbles.keys.addKeyPressListener( 'r', function() { window.location = detail_url + '#publish'; }); kibbles.keys.addKeyPressListener('j', gotoNextPage); kibbles.keys.addKeyPressListener('k', gotoPreviousPage); kibbles.keys.addKeyPressListener('h', toggleComments); } </script> <script src="http://www.gstatic.com/codesite/ph/6432456761710229989/js/code_review_scripts.js";></script> <script type="text/javascript"> function showPublishInstructions() { var element = document.getElementById('review_instr'); if (element) { element.className = 'opened'; } } var codereviews; function revsOnLoadHandler() { // register our source container with the commenting code var paths = {'svn98': '/source/mpi_test.c'} codereviews = CR_controller.setup( {"profileUrl":["/u/@UhFXRVJWBRJGVwN8/"],"token":"37184c5d629ad5b3864d886a93928b17","assetHostPath":"http://www.gstatic.com/codesite/ph","domainName":null,"assetVersionPath":"http://www.gstatic.com/codesite/ph/6432456761710229989","projectHomeUrl":"/p/pypar","relativeBaseUrl":"","projectName":"pypar","loggedInUserEmail":"ole.moller.niel...@gmail.com"}, '', 'svn98', paths, CR_BrowseIntegrationFactory); // register our source container with the commenting code // in this case we're registering the container and the revison // associated with the contianer which may be the primary revision // or may be a previous revision against which the primary revision // of the file is being compared. codereviews.registerSourceContainer(document.getElementById('lines'), 'svn98'); codereviews.registerActivityListener(CR_ActivityType.REVEAL_DRAFT_PLATE, showPublishInstructions); codereviews.registerActivityListener(CR_ActivityType.REVEAL_PUB_PLATE, pubRevealed); codereviews.registerActivityListener(CR_ActivityType.REVEAL_DRAFT_PLATE, draftRevealed); codereviews.registerActivityListener(CR_ActivityType.DISCARD_DRAFT_COMMENT, draftDestroyed); var initialized = true; reloadCursors(); } window.onload = function() {keysOnLoadHandler(); revsOnLoadHandler();}; </script> <script type="text/javascript" src="http://www.gstatic.com/codesite/ph/6432456761710229989/js/dit_scripts.js";></script> <script type="text/javascript" src="http://www.gstatic.com/codesite/ph/6432456761710229989/js/ph_core.js";></script> <script type="text/javascript" src="/js/codesite_product_dictionary_ph.pack.04102009.js"></script> </div> <div id="footer" dir="ltr"> <div class="text"> ©2011 Google - <a href="/projecthosting/terms.html">Terms</a> - <a href="http://www.google.com/privacy.html";>Privacy</a> - <a href="/p/support/">Project Hosting Help</a> </div> </div> <div class="hostedBy" style="margin-top: -20px;"> <span style="vertical-align: top;">Powered by <a 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