<div dir="ltr">You want to subscribe to the "user" list and post your messages there. I'll look for your messages on that board. </div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0);font-size:small">Best,</span><br></div><div><span style="font-size:small"><font color="#000000">Glen</font></span></div><div><span style="color:rgb(7,55,99);font-size:small"><br></span></div><div><span style="color:rgb(7,55,99);font-size:small">==========================================</span></div><div><div style="font-size:13px"><font color="#073763">Glen MacLachlan, PhD</font></div></div><div style="font-size:13px"><div><font color="#073763"><i>HPC Specialist </i><i>for Physical Sciences &<br></i></font></div><div><font color="#073763"><i>Professorial Lecturer, Data Sciences<br></i></font></div></div></div></div></div></div></div></div></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Office of Technology Services</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">The George Washington University</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">725 21st Street</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Washington, DC 20052</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Suite 211, Corcoran Hall</font></div></div></div></div></div></div></div></div></div></div></blockquote><span style="color:rgb(7,55,99);font-size:small">==========================================</span><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div style="font-size:13px"><div><br></div></div></div></blockquote><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(102,102,102)"><span style="border-collapse:collapse"><div style="font-size:13px;font-family:arial,sans-serif"><div><br></div></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 22, 2016 at 2:15 PM, Cohen, Ronald <span dir="ltr"><<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Oh--thank you so much! I will write there.<div><br></div><div>Ron</div><div><br></div></div><div class="gmail_extra"><span class=""><br clear="all"><div><div>---<br>Ronald Cohen<br>Geophysical Laboratory<br>Carnegie Institution<br>5251 Broad Branch Rd., N.W.<br>Washington, D.C. 20015<br><a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a><br>office: <a href="tel:202-478-8937" value="+12024788937" target="_blank">202-478-8937</a><br>skype: ronaldcohen<br><a href="https://twitter.com/recohen3" target="_blank">https://twitter.com/recohen3</a><br><a href="https://www.linkedin.com/profile/view?id=163327727" target="_blank">https://www.linkedin.com/profile/view?id=163327727</a><br></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Tue, Mar 22, 2016 at 3:13 PM, Glen MacLachlan <span dir="ltr"><<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">No, no...don't misunderstand. I don't mind helping -- I want to figure this out too! Just saying we might want to take it over to the OpenMPI message boards. There you'll get hundreds of OpenMPI experts looking at your problem.<div><br></div><div><a href="https://www.open-mpi.org/faq/" target="_blank">https://www.open-mpi.org/faq/</a><br></div><div><a href="https://www.open-mpi.org/community/lists/ompi.php" target="_blank">https://www.open-mpi.org/community/lists/ompi.php</a><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0);font-size:small">Best,</span><br></div><div><span style="font-size:small"><font color="#000000">Glen</font></span></div><div><span style="color:rgb(7,55,99);font-size:small"><br></span></div><div><span style="color:rgb(7,55,99);font-size:small">==========================================</span></div><div><div style="font-size:13px"><font color="#073763">Glen MacLachlan, PhD</font></div></div><div style="font-size:13px"><div><font color="#073763"><i>HPC Specialist </i><i>for Physical Sciences &<br></i></font></div><div><font color="#073763"><i>Professorial Lecturer, Data Sciences<br></i></font></div></div></div></div></div></div></div></div></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Office of Technology Services</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">The George Washington University</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">725 21st Street</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Washington, DC 20052</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Suite 211, Corcoran Hall</font></div></div></div></div></div></div></div></div></div></div></blockquote><span style="color:rgb(7,55,99);font-size:small">==========================================</span><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div style="font-size:13px"><div><br></div></div></div></blockquote><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(102,102,102)"><span style="border-collapse:collapse"><div style="font-size:13px;font-family:arial,sans-serif"><div><br></div></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 22, 2016 at 2:09 PM, Cohen, Ronald <span dir="ltr"><<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Yes, thank you so much. Basically I am getting mud even with 2 nodes, so using more could not be better. I understand it is off topic, so won't bother you. I have to get this working before I can worry about cp2k performance!<div><br></div><div>Ron</div><div><br></div></div><div class="gmail_extra"><span><br clear="all"><div><div>---<br>Ronald Cohen<br>Geophysical Laboratory<br>Carnegie Institution<br>5251 Broad Branch Rd., N.W.<br>Washington, D.C. 20015<br><a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a><br>office: <a href="tel:202-478-8937" value="+12024788937" target="_blank">202-478-8937</a><br>skype: ronaldcohen<br><a href="https://twitter.com/recohen3" target="_blank">https://twitter.com/recohen3</a><br><a href="https://www.linkedin.com/profile/view?id=163327727" target="_blank">https://www.linkedin.com/profile/view?id=163327727</a><br></div></div>
<br></span><div><div><div class="gmail_quote">On Tue, Mar 22, 2016 at 3:07 PM, Glen MacLachlan <span dir="ltr"><<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Ron, <div><br></div><div>I think this is sort of off topic for the CP2K folks and more along the lines of OpenMPI but I'm happy to continue the discussion -- I'm afraid they might ask us to take it elsewhere though. </div><div><br></div><div>So you want to do a couple of things<div><ol><li> vary the number of tasks and look for scaling -- you need to do this across multiple nodes to see what affect infiniband is having -- I assume you know how to ask your scheduler to distribute the tasks across multiple nodes. <br></li><li>look for the throughput that you expect to be getting from your infiniband fabric. Did you mention what inifiniband you are running? qdr? fdr? You can compare the NPB benchmarks for your ib and ethernet networks. Do you know what your ethernet network throughput is? gigE? 10gig? You may want to have a look at this benchmark report that used NPB and NWChem, among others: <a href="http://www.dell.com/Downloads/Global/Power/ps1q10-20100215-Mellanox.pdf" target="_blank">http://www.dell.com/Downloads/Global/Power/ps1q10-20100215-Mellanox.pdf</a></li></ol><div>Also, not having an admin handy or root access is not to bad of an impediment. You can stand up your own instance of openmpi without special privileges. Before you start chasing too many benchmarks (which can be difficult to resist) you may want to spin up your own OpenMPI instance and see if you can beat the ethernet performance. </div></div></div><div><br></div><div>By the way, when you type <font face="monospace, monospace">ifconfig </font><font face="arial, helvetica, sans-serif">do you see an interface that looks like </font><font face="monospace, monospace">ib0</font><font face="arial, helvetica, sans-serif"> or </font><font face="monospace, monospace">ib1 </font><font face="arial, helvetica, sans-serif">or something like that?</font></div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0);font-size:small">Best,</span><br></div><div><span style="font-size:small"><font color="#000000">Glen</font></span></div><div><span style="color:rgb(7,55,99);font-size:small"><br></span></div><div><span style="color:rgb(7,55,99);font-size:small">==========================================</span></div><div><div style="font-size:13px"><font color="#073763">Glen MacLachlan, PhD</font></div></div><div style="font-size:13px"><div><font color="#073763"><i>HPC Specialist </i><i>for Physical Sciences &<br></i></font></div><div><font color="#073763"><i>Professorial Lecturer, Data Sciences<br></i></font></div></div></div></div></div></div></div></div></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Office of Technology Services</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">The George Washington University</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">725 21st Street</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Washington, DC 20052</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Suite 211, Corcoran Hall</font></div></div></div></div></div></div></div></div></div></div></blockquote><span style="color:rgb(7,55,99);font-size:small">==========================================</span><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div style="font-size:13px"><div><br></div></div></div></blockquote><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(102,102,102)"><span style="border-collapse:collapse"><div style="font-size:13px;font-family:arial,sans-serif"><div><br></div></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 22, 2016 at 1:05 PM, Cohen, Ronald <span dir="ltr"><<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Glen,<div><br></div><div>I made NPB. Which test do you recommend me running? I have run several and it is not clear what to look for.</div><div><br></div><div>Sincerely,</div><div><br></div><div>Ron</div><div><br></div></div><div class="gmail_extra"><span><br clear="all"><div><div>---<br>Ronald Cohen<br>Geophysical Laboratory<br>Carnegie Institution<br>5251 Broad Branch Rd., N.W.<br>Washington, D.C. 20015<br><a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a><br>office: <a href="tel:202-478-8937" value="+12024788937" target="_blank">202-478-8937</a><br>skype: ronaldcohen<br><a href="https://twitter.com/recohen3" target="_blank">https://twitter.com/recohen3</a><br><a href="https://www.linkedin.com/profile/view?id=163327727" target="_blank">https://www.linkedin.com/profile/view?id=163327727</a><br></div></div>
<br></span><div><div><div class="gmail_quote">On Tue, Mar 22, 2016 at 12:33 PM, Glen MacLachlan <span dir="ltr"><<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Check with your admin to see what networks are available but if you disable tcp using<font face="monospace, monospace"> </font><span style="color:rgb(0,0,0)"><font face="monospace, monospace">mpirun --mca btl ^tcp</font> then you should be giving MPI no choice but to use IB. You can also increase the verbosity by adding<font face="monospace, monospace"> </font></span><span style="color:rgb(0,0,0)"><font face="monospace, monospace">--mca btl_openib_verbose 1.</font></span><div><span style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif">Also, did you run </font><font face="monospace, monospace">ompi_info --all</font><font face="arial, helvetica, sans-serif"> as Andreas suggested? </font></span></div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0);font-size:small">Best,</span><br></div><div><span style="font-size:small"><font color="#000000">Glen</font></span></div><div><span style="color:rgb(7,55,99);font-size:small"><br></span></div><div><span style="color:rgb(7,55,99);font-size:small">==========================================</span></div><div><div style="font-size:13px"><font color="#073763">Glen MacLachlan, PhD</font></div></div><div style="font-size:13px"><div><font color="#073763"><i>HPC Specialist </i><i>for Physical Sciences &<br></i></font></div><div><font color="#073763"><i>Professorial Lecturer, Data Sciences<br></i></font></div></div></div></div></div></div></div></div></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Office of Technology Services</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">The George Washington University</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">725 21st Street</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Washington, DC 20052</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Suite 211, Corcoran Hall</font></div></div></div></div></div></div></div></div></div></div></blockquote><span style="color:rgb(7,55,99);font-size:small">==========================================</span><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div style="font-size:13px"><div><br></div></div></div></blockquote><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(102,102,102)"><span style="border-collapse:collapse"><div style="font-size:13px;font-family:arial,sans-serif"><div><br></div></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 22, 2016 at 11:21 AM, Cohen, Ronald <span dir="ltr"><<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">OK, I ran xhpl with those flags and got the same 1 GF performance as without. So I guess my openmpi is not using ib. I wonder how to turn that on! My config.log for the build seems to show that it found infiniband. I attached it in case you have time to look. Thank you so much!<div><br></div><div>Ron</div><div><br></div></div><div class="gmail_extra"><span><br clear="all"><div><div>---<br>Ronald Cohen<br>Geophysical Laboratory<br>Carnegie Institution<br>5251 Broad Branch Rd., N.W.<br>Washington, D.C. 20015<br><a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a><br>office: <a href="tel:202-478-8937" value="+12024788937" target="_blank">202-478-8937</a><br>skype: ronaldcohen<br><a href="https://twitter.com/recohen3" target="_blank">https://twitter.com/recohen3</a><br><a href="https://www.linkedin.com/profile/view?id=163327727" target="_blank">https://www.linkedin.com/profile/view?id=163327727</a><br></div></div>
<br></span><div><div><div class="gmail_quote">On Tue, Mar 22, 2016 at 12:12 PM, Glen MacLachlan <span dir="ltr"><<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Yeah, the ^ is a regular expression character that means ignore what comes after -- think of it as a negation. <div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0);font-size:small">Best,</span><br></div><div><span style="font-size:small"><font color="#000000">Glen</font></span></div><div><span style="color:rgb(7,55,99);font-size:small"><br></span></div><div><span style="color:rgb(7,55,99);font-size:small">==========================================</span></div><div><div style="font-size:13px"><font color="#073763">Glen MacLachlan, PhD</font></div></div><div style="font-size:13px"><div><font color="#073763"><i>HPC Specialist </i><i>for Physical Sciences &<br></i></font></div><div><font color="#073763"><i>Professorial Lecturer, Data Sciences<br></i></font></div></div></div></div></div></div></div></div></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Office of Technology Services</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">The George Washington University</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">725 21st Street</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Washington, DC 20052</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Suite 211, Corcoran Hall</font></div></div></div></div></div></div></div></div></div></div></blockquote><span style="color:rgb(7,55,99);font-size:small">==========================================</span><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div style="font-size:13px"><div><br></div></div></div></blockquote><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(102,102,102)"><span style="border-collapse:collapse"><div style="font-size:13px;font-family:arial,sans-serif"><div><br></div></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 22, 2016 at 11:04 AM, Cohen, Ronald <span dir="ltr"><<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thank you so much. It is a bit difficult because I did not set up this machine and do not have root access, but I know it is a mess. I backed up to just try the HPL benchmark.<div>I am finding 100 GFLOPS one node performance on N=2000 and 16 cores, and 1.5 GFLOPS using two nodes, 8 cores per node. So there is definately something really wrong. I need to getthis working before I can worry about threads or cp2k.</div><div>Was that a caret in your command above:</div><div><br></div><div><span style="font-family:monospace,monospace;font-size:12.8px">mpirun --mca btl ^tcp</span><br></div><div><span style="font-family:monospace,monospace;font-size:12.8px"><br></span></div><div><span style="font-family:monospace,monospace;font-size:12.8px">?</span></div><div><span style="font-family:monospace,monospace;font-size:12.8px"><br></span></div><div><font face="monospace, monospace"><span style="font-size:12.8px">I looked through my openmpi build and it seems to have found the infiniband includes such as they exist on the machine, but I could not the expected mxm or Mellanox drivers anywhere on the machine. </span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px"><br></span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px">I am CCing Peter Fox, the person who volunteers his time for this machine, and who has root access!</span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px"><br></span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px">Sincerely,</span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px"><br></span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px">Ron</span></font></div><div><font face="monospace, monospace"><span style="font-size:12.8px"><br></span></font></div></div><div class="gmail_extra"><span><br clear="all"><div><div>---<br>Ronald Cohen<br>Geophysical Laboratory<br>Carnegie Institution<br>5251 Broad Branch Rd., N.W.<br>Washington, D.C. 20015<br><a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a><br>office: <a href="tel:202-478-8937" value="+12024788937" target="_blank">202-478-8937</a><br>skype: ronaldcohen<br><a href="https://twitter.com/recohen3" target="_blank">https://twitter.com/recohen3</a><br><a href="https://www.linkedin.com/profile/view?id=163327727" target="_blank">https://www.linkedin.com/profile/view?id=163327727</a><br></div></div>
<br></span><div><div><div class="gmail_quote">On Tue, Mar 22, 2016 at 10:32 AM, Glen MacLachlan <span dir="ltr"><<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi Ron, </div><div><br></div>There's a chance that OpenMPI wasn't configured to use IB properly. Why don't you disable tcp and see if you are using IB? It's easy<blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><font face="monospace, monospace">mpirun --mca btl ^tcp ...</font></div></blockquote><div><br></div><div>Regarding OpenMP:</div><div>I'm not sure we're converging on the same discussion anymore but setting OMP_NUM_THREADS=1 does <u>not</u> disable multithreading overhead -- you need to compile without the fopenmp to get a measure of true single thread performance. </div><div><br></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="color:rgb(0,0,0);font-size:small">Best,</span><br></div><div><span style="font-size:small"><font color="#000000">Glen</font></span></div><div><span style="color:rgb(7,55,99);font-size:small"><br></span></div><div><span style="color:rgb(7,55,99);font-size:small">==========================================</span></div><div><div style="font-size:13px"><font color="#073763">Glen MacLachlan, PhD</font></div></div><div style="font-size:13px"><div><font color="#073763"><i>HPC Specialist </i><i>for Physical Sciences &<br></i></font></div><div><font color="#073763"><i>Professorial Lecturer, Data Sciences<br></i></font></div></div></div></div></div></div></div></div></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Office of Technology Services</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">The George Washington University</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">725 21st Street</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Washington, DC 20052</font></div></div></div></div></div></div></div></div></div></div><div><div><div><div><div><div><div><div><div><div style="font-size:13px"><font color="#073763">Suite 211, Corcoran Hall</font></div></div></div></div></div></div></div></div></div></div></blockquote><span style="color:rgb(7,55,99);font-size:small">==========================================</span><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div style="font-size:13px"><div><br></div></div></div></blockquote><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(102,102,102)"><span style="border-collapse:collapse"><div style="font-size:13px;font-family:arial,sans-serif"><div><br></div></div></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Mar 21, 2016 at 5:05 PM, Ronald Cohen <span dir="ltr"><<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>According to my experience in general, or the cp2k web pages in particular that is not the case. Please see the performance page for cp2k. The problem I am sure now is with the openmpi build not using the proper infiniband libraries or drivers.</div><div><br></div><div>Thank you!</div><div><br></div><div>Ron</div><div><br>Sent from my iPad</div><div><div><div><br>On Mar 21, 2016, at 5:36 PM, Glen MacLachlan <<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>> wrote:<br><br></div><blockquote type="cite"><div><p dir="ltr">It's hard to talk about the performance when you set OMP_NUM_THREADS = 1 because there is so much overhead associated with OpenMP that launching 1 thread almost always is a performance killer. In fact, OMP_NUM_THREADS=1 never rivals single-threaded performance-wise because of that overhead. No one ever sets OMP_NUM_THREADS=1 unless they are playing around...We never do that in production jobs. How about when you scale up to 4 or 8 threads? </p>
<p dir="ltr">Glen</p>
<p dir="ltr">P.S. I see you're in DC...so am I. I support CP2K for the chemists at GWU. Hope you aren't using Metro to get around the DMV :p</p>
<div class="gmail_quote">On Mar 21, 2016 5:11 PM, "Cohen, Ronald" <<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Yes I am using hybrid mode. But even if I set OMP_NUM_THREADS=1 performance is terrible.</div><div class="gmail_extra"><br clear="all"><div><div>---<br>Ronald Cohen<br>Geophysical Laboratory<br>Carnegie Institution<br>5251 Broad Branch Rd., N.W.<br>Washington, D.C. 20015<br><a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a><br>office: <a href="tel:202-478-8937" value="+12024788937" target="_blank">202-478-8937</a><br>skype: ronaldcohen<br><a href="https://twitter.com/recohen3" target="_blank">https://twitter.com/recohen3</a><br><a href="https://www.linkedin.com/profile/view?id=163327727" target="_blank">https://www.linkedin.com/profile/view?id=163327727</a><br></div></div>
<br><div class="gmail_quote">On Mon, Mar 21, 2016 at 5:04 PM, Glen MacLachlan <span dir="ltr"><<a href="mailto:mac...@gwu.edu" target="_blank">mac...@gwu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Are you conflating MPI with OpenMP? OMP_NUM_THREADS sets the number of threads used by OpenMP and OpenMP doesn't work on a distributed memory environment unless you piggyback on MPI which would be a hybrid use and I'm not sure CP2K ever worked optimally in hybrid mode or at least that's what I've gotten from reading the comments on the source code. </p>
<p dir="ltr">As for MPI, are you sure your MPI stack was compiled with IB bindings? I had similar issues and the problem was that I wasn't actually using IB. If you can, disable eth and leave only IB and see what happens.</p>
<p dir="ltr">Glen </p>
<div class="gmail_quote">On Mar 21, 2016 4:48 PM, "Ronald Cohen" <<a href="mailto:rco...@carnegiescience.edu" target="_blank">rco...@carnegiescience.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div style="font-family:arial,sans-serif;font-size:12.8px">On the dco machine deepcarbon I find decent single node mpi performnace, but running on the same number of processors across two nodes is terrible, even with the infiniband interconect. This is the cp2k H2O-64 benchmark:</div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"> </div><div style="font-family:arial,sans-serif;font-size:12.8px">On 16 cores on 1 node: total time 530 seconds</div><div style="font-family:arial,sans-serif;font-size:12.8px"><div> SUBROUTINE CALLS ASD SELF TIME TOTAL TIME</div><div> MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM</div><div> CP2K 1 1.0 0.015 0.019 530.306 530.306</div></div><div style="font-family:arial,sans-serif;font-size:12.8px"><div> - -</div><div> - MESSAGE PASSING PERFORMANCE -</div><div> - -</div><div> -------------------------------------------------------------------------------</div><div><br></div><div> ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]</div><div> MP_Group 5 0.000</div><div> MP_Bcast 4103 0.029 44140. 6191.05</div><div> MP_Allreduce 21860 7.077 263. 0.81</div><div> MP_Gather 62 0.008 320. 2.53</div><div> MP_Sync 54 0.001</div><div> MP_Alltoall 19407 26.839 648289. 468.77</div><div> MP_ISendRecv 21600 0.091 94533. 22371.25</div><div> MP_Wait 238786 50.545</div><div> MP_comm_split 50 0.004</div><div> MP_ISend 97572 0.741 239205. 31518.68</div><div> MP_IRecv 97572 8.605 239170. 2711.98</div><div> MP_Memory 167778 45.018</div><div> -------------------------------------------------------------------------------</div></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px">on 16 cores on 2 nodes: total time 5053 seconds !!</div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"><div>SUBROUTINE CALLS ASD SELF TIME TOTAL TIME</div><div> MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM</div><div> CP2K 1 1.0 0.311 0.363 5052.904 5052.909</div></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"><div>-------------------------------------------------------------------------------</div><div> - -</div><div> - MESSAGE PASSING PERFORMANCE -</div><div> - -</div><div> -------------------------------------------------------------------------------</div><div><br></div><div> ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]</div><div> MP_Group 5 0.000</div><div> MP_Bcast 4119 0.258 43968. 700.70</div><div> MP_Allreduce 21892 1546.186 263. 0.00</div><div> MP_Gather 62 0.049 320. 0.40</div><div> MP_Sync 54 0.071</div><div> MP_Alltoall 19407 1507.024 648289. 8.35</div><div> MP_ISendRecv 21600 0.104 94533. 19656.44</div><div> MP_Wait 238786 513.507</div><div> MP_comm_split 50 4.096</div><div> MP_ISend 97572 1.102 239206. 21176.09</div><div> MP_IRecv 97572 2.739 239171. 8520.75</div><div> MP_Memory 167778 18.845</div><div> -------------------------------------------------------------------------------</div></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px">Any ideas? The code was built with the latest gfortran and I built all of the dependencies, using this arch file.</div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:arial,sans-serif;font-size:12.8px"><div style="font-size:12.8px">CC = gcc</div><div style="font-size:12.8px">CPP =</div><div style="font-size:12.8px">FC = mpif90</div><div style="font-size:12.8px">LD = mpif90</div><div style="font-size:12.8px">AR = ar -r</div><div style="font-size:12.8px">PREFIX = /home/rcohen</div><div style="font-size:12.8px">FFTW_INC = $(PREFIX)/include</div><div style="font-size:12.8px">FFTW_LIB = $(PREFIX)/lib</div><div style="font-size:12.8px">LIBINT_INC = $(PREFIX)/include</div><div style="font-size:12.8px">LIBINT_LIB = $(PREFIX)/lib</div><div style="font-size:12.8px">LIBXC_INC = $(PREFIX)/include</div><div style="font-size:12.8px">LIBXC_LIB = $(PREFIX)/lib</div><div style="font-size:12.8px">GCC_LIB = $(PREFIX)/gcc-trunk/lib</div><div style="font-size:12.8px">GCC_LIB64 = $(PREFIX)/gcc-trunk/lib64</div><div style="font-size:12.8px">GCC_INC = $(PREFIX)/gcc-trunk/include</div><div style="font-size:12.8px">DFLAGS = -D__FFTW3 -D__LIBINT -D__LIBXC2\</div><div style="font-size:12.8px"> -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4\</div><div style="font-size:12.8px"> -D__parallel -D__SCALAPACK -D__HAS_smm_dnn -D__ELPA3 </div><div style="font-size:12.8px">CPPFLAGS =</div><div style="font-size:12.8px">FCFLAGS = $(DFLAGS) -O2 -ffast-math -ffree-form -ffree-line-length-none\</div><div style="font-size:12.8px"> -fopenmp -ftree-vectorize -funroll-loops\</div><div style="font-size:12.8px"> -mtune=native \</div><div style="font-size:12.8px"> -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC) -I$(MKLROOT)/include \</div><div style="font-size:12.8px"> -I$(GCC_INC) -I$(PREFIX)/include/elpa_openmp-2015.11.001/modules</div><div style="font-size:12.8px">LIBS = \</div><div style="font-size:12.8px"> $(PREFIX)/lib/libscalapack.a $(PREFIX)/lib/libsmm_dnn_sandybridge-2015-11-10.a \</div><div style="font-size:12.8px"> $(FFTW_LIB)/libfftw3.a\</div><div style="font-size:12.8px"> $(FFTW_LIB)/libfftw3_threads.a\</div><div style="font-size:12.8px"> $(LIBXC_LIB)/libxcf90.a\</div><div style="font-size:12.8px"> $(LIBXC_LIB)/libxc.a\</div><div style="font-size:12.8px"> $(PREFIX)/lib/liblapack.a $(PREFIX)/lib/libtmglib.a $(PREFIX)/lib/libgomp.a \</div><div style="font-size:12.8px"> $(PREFIX)/lib/libderiv.a $(PREFIX)/lib/libint.a -lelpa_openmp -lgomp -lopenblas</div><div style="font-size:12.8px">LDFLAGS = $(FCFLAGS) -L$(GCC_LIB64) -L$(GCC_LIB) -static-libgfortran -L$(PREFIX)/lib </div><div><br></div><div>It was run with <span style="font-size:12.8px">OMP_NUM_THREADS=2 on the two nodes</span> and OMP_NUM_THREADS=1 on the one node.</div><div>Running with OMP_NUM_THREADS=1 on two nodes .</div><div><br></div><div>I am now checking whether <span style="font-size:12.8px">OMP_NUM_THREADS=1 on two nodes is faster than </span><span style="font-size:12.8px">OMP_NUM_THREADS=2 , but I do not think so.</span></div><div><br></div><div>Ron Cohen</div><div><br></div></div><div style="font-family:arial,sans-serif;font-size:12.8px"><br></div><span><font color="#888888"><div><br></div></font></span></div><span><font color="#888888">
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