Hi David,<br><br>I built the pnetcdf 1.3.0-pre1 release on bluewaters and<br>ran the nf_test provided with that package. It exhibits the same issues with nfmpi_create and nfmpi_open that I am seeing from the installed parallel-netcdf-1.2.0 and my application. <br>
I have opened ticket <a id="key-val" rel="13055" href="https://ncsa-jira.ncsa.illinois.edu/browse/BWDSPCH-298">BWDSPCH-298</a> on bluewaters to track this issue. <br><br><div class="gmail_quote">On Fri, May 11, 2012 at 6:50 PM, David Knaak <span dir="ltr"><<a href="mailto:knaak@cray.com" target="_blank">knaak@cray.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Jim,<br>
<br>
I'm not intimate with pnetcdf but the stack trace entries look a little<br>
strange to me. In particular:<br>
<br>
#10<br>
count=0x1527daa0, stride=0x0<br>
<br>
#13<br>
start=0x7fffffff3750, count=0x7fffffff3750<br>
<br>
Could it be that the high level routine is being called with a bad<br>
argument?<br>
<br>
Just a thought.<br>
<span class="HOEnZb"><font color="#888888"><br>
David<br>
</font></span><div class="im"><br>
On Fri, May 11, 2012 at 05:37:24PM -0600, Jim Edwards wrote:<br>
</div><div><div class="h5">> Hi David,<br>
><br>
> I've updated to the 5.2.5 mpich2 on bluewaters and now get a different problem,<br>
> it happens earlier in the code so I think that this worked in the older<br>
> version, here is a partial stack trace from the core file on 16000 tasks.<br>
> I'll try on Monday to reproduce this on a smaller number of tasks. Can I<br>
> send you more info when I get it?<br>
><br>
> #0 memcpy () at ../sysdeps/x86_64/memcpy.S:102<br>
> #1 0x0000000000c25b03 in MPIDI_CH3U_Buffer_copy ()<br>
> #2 0x0000000000bc91ae in MPIDI_Isend_self ()<br>
> #3 0x0000000000bc5ef4 in MPID_Isend ()<br>
> #4 0x0000000000be4b2b in PMPI_Isend ()<br>
> #5 0x0000000000b9439a in ADIOI_CRAY_R_Exchange_data ()<br>
> #6 0x0000000000b9503d in ADIOI_CRAY_Read_and_exch ()<br>
> #7 0x0000000000b957ca in ADIOI_CRAY_ReadStridedColl ()<br>
> #8 0x0000000000b7ea69 in MPIOI_File_read_all ()<br>
> #9 0x0000000000b7eab6 in PMPI_File_read_all ()<br>
> #10 0x0000000000b3d7ce in ncmpii_getput_vars (ncp=0x107192b0, varp=0x109ee340,<br>
> start=0x15269910, count=0x1527daa0, stride=0x0,<br>
> buf=0x155f5480, bufcount=245561, datatype=-871890885, rw_flag=1, io_method=<br>
> 1) at ./getput_vars.c:741<br>
> #11 0x0000000000b39804 in ncmpi_get_vara_all (ncid=1, varid=59, start=<br>
> 0x15269910, count=0x1527daa0, buf=0x155f5480,<br>
> bufcount=245561, datatype=-871890885) at ./getput_vara.c:435<br>
> #12 0x0000000000b092c6 in nfmpi_get_vara_all_ (v1=0x33e8dd8, v2=0x33e89a0, v3=<br>
> 0x418d500, v4=0x418c500, v5=0x155f5480,<br>
> v6=0x1e72e10, v7=0x1e72e04) at ./get_vara_allf.c:57<br>
> #13 0x00000000007c0524 in pionfread_mod::read_nfdarray_double (file=..., iobuf=<br>
> 0x155f5480, vardesc=..., iodesc=...,<br>
> start=0x7fffffff3750, count=0x7fffffff3750)<br>
><br>
><br>
> On Fri, May 11, 2012 at 5:25 PM, Jim Edwards <<a href="mailto:jedwards@ucar.edu">jedwards@ucar.edu</a>> wrote:<br>
><br>
> David,<br>
><br>
> I will give this a try, thanks.<br>
><br>
><br>
> On Fri, May 11, 2012 at 5:15 PM, David Knaak <<a href="mailto:knaak@cray.com">knaak@cray.com</a>> wrote:<br>
><br>
> Rob,<br>
><br>
> I suggested taking the discussion off line to not bother those not<br>
> interested in the Cray specifics. But if you think those on the list<br>
> are either interested, or don't consider it a bother, I can certainly<br>
> use the full list.<br>
><br>
> All,<br>
><br>
> In the MPT 5.4.0 release, I made some changes to MPI_File_open to<br>
> improve scalability. Because of these changes and previous changes<br>
> I had made (for added functionality, not because of any bugs), the<br>
> code was getting very messy. In fact, I introduced a bug or 2 with<br>
> these changes. So in 5.4.3, I significantly restructured the code<br>
> for better maintainability, fixed the bugs (that I knew of) and made<br>
> more scalability changes.<br>
><br>
> Jim,<br>
><br>
> The NCSA's "ESS" has the 5.4.2 version of Cray's MPI implementation as<br>
> default. The "module list" command output that you included shows:<br>
><br>
> 3) xt-mpich2/5.4.2<br>
><br>
> The "module avail xt-mpch2" command shows what other versions are<br>
> available:<br>
><br>
> h2ologin2 25=>module avail xt-mpich2<br>
> --------------------- /opt/cray/modulefiles ---------------------<br>
> xt-mpich2/5.4.2(default) xt-mpich2/5.4.4 xt-mpich2/5.4.5<br>
><br>
> Would you switch to 5.4.5, relink, and try again?<br>
><br>
> h2ologin2 25=>module swap xt-mpich2/5.4.2 xt-mpich2/5.4.5<br>
><br>
> Thanks.<br>
> David<br>
><br>
><br>
> On Fri, May 11, 2012 at 12:54:39PM -0500, Rob Latham wrote:<br>
> > On Fri, May 11, 2012 at 11:46:25AM -0500, David Knaak wrote:<br>
> > > Jim,<br>
> > ><br>
> > > Since you are having this problem on a Cray system, please open a<br>
> Cray<br>
> > > bug report against MPI and I will look at it. We can take further<br>
> > > discussions off line.<br>
> ><br>
> > Oh, howdy David! forgot you were on the list. Thanks for keeping an<br>
> > eye on things.<br>
> ><br>
> > the pnetcdf list is pretty low-traffic these days, but we have an<br>
> > awful lot of users in a cray and Lustre environment. If you'd<br>
> rather<br>
> > discuss cray specific stuff elsewhere, I'd understand, but please let<br>
> > us know what you figure out.<br>
> ><br>
> > ==rob<br>
> ><br>
> > > Thanks.<br>
> > > David<br>
> > ><br>
> > > On Fri, May 11, 2012 at 10:03:28AM -0600, Jim Edwards wrote:<br>
> > > ><br>
> > > ><br>
> > > > On Fri, May 11, 2012 at 9:43 AM, Rob Latham <<a href="mailto:robl@mcs.anl.gov">robl@mcs.anl.gov</a>><br>
> wrote:<br>
> > > ><br>
> > > > On Thu, May 10, 2012 at 03:28:57PM -0600, Jim Edwards wrote:<br>
> > > > > This occurs on the ncsa machine bluewaters. I am using<br>
> pnetcdf1.2.0 and<br>
> > > > > pgi 11.10.0<br>
> > > ><br>
> > > > need one more bit of information: the version of MPT you are<br>
> using.<br>
> > > ><br>
> > > ><br>
> > > > Sorry, what's mpt? MPI?<br>
> > > > Currently Loaded Modulefiles:<br>
> > > > 1) modules/<a href="http://3.2.6.6" target="_blank">3.2.6.6</a> 9)<br>
> > > > user-paths 17) xpmem/<br>
> 0.1-2.0400.31280.3.1.gem<br>
> > > > 2) xtpe-network-gemini 10) pgi/<br>
> > > > 11.10.0 18) xe-sysroot/4.0.46<br>
> > > > 3) xt-mpich2/5.4.2 11) xt-libsci/<br>
> > > > 11.0.04 19) xt-asyncpe/5.07<br>
> > > > 4) xtpe-interlagos 12) udreg/<br>
> > > > 2.3.1-1.0400.4264.3.1.gem 20) atp/1.4.1<br>
> > > > 5) eswrap/1.0.12 13) ugni/<br>
> > > > 2.3-1.0400.4374.4.88.gem 21) PrgEnv-pgi/4.0.46<br>
> > > > 6) torque/2.5.10 14) pmi/<br>
> > > > 3.0.0-1.0000.8661.28.2807.gem 22) hdf5-parallel/1.8.7<br>
> > > > 7) moab/6.1.5 15) dmapp/<br>
> > > > 3.2.1-1.0400.4255.2.159.gem 23) netcdf-hdf5parallel/4.1.3<br>
> > > > 8) scripts 16) gni-headers/<br>
> > > > 2.1-1.0400.4351.3.1.gem 24) parallel-netcdf/1.2.0<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > > The issue is that calling nfmpi_createfile would sometimes<br>
> result in an<br>
> > > > > error:<br>
> > > > ><br>
> > > > > MPI_File_open : Other I/O error , error stack:<br>
> > > > > (unknown)(): Other I/O error<br>
> > > > > 126: MPI_File_open : Other I/O error , error stack:<br>
> > > > > (unknown)(): Other I/O error<br>
> > > > > Error on create : 502 -32<br>
> > > > ><br>
> > > > > The error appears to be intermittent and I could not get it<br>
> to occur at<br>
> > > > all<br>
> > > > > on a small number of tasks (160) but it occurs with high<br>
> frequency when<br>
> > > > > using a larger number of tasks (>=1600). I traced the<br>
> problem to the<br>
> > > > use<br>
> > > > > of nf_clobber in the mode argument, removing the nf_clobber<br>
> seems to have<br>
> > > > > solved the problem and I think that create implies clobber<br>
> anyway doesn't<br>
> > > > > it?<br>
> > > ><br>
> > > > > Can someone who knows what is going on under the covers<br>
> enlighten me<br>
> > > > > with some understanding of this issue? I suspect that one<br>
> task is<br>
> > > > trying<br>
> > > > > to clobber the file that another has just created or<br>
> something of that<br>
> > > > > nature.<br>
> > > ><br>
> > > > Unfortunately, "under the covers" here means "inside the<br>
> MPI-IO<br>
> > > > library", which we don't have access to.<br>
> > > ><br>
> > > > in the create case we call MPI_File_open with "MPI_MODE_RDWR<br>
> |<br>
> > > > MPI_MODE_CREATE", and if noclobber set, we add<br>
> MPI_MODE_EXCL.<br>
> > > ><br>
> > > > OK, so that's pnetcdf. What's going on in MPI-IO? Well,<br>
> cray's based<br>
> > > > their MPI-IO off of our ROMIO, but I'm not sure which<br>
> version.<br>
> > > ><br>
> > > > Let me cook up a quick MPI-IO-only test case you can run to<br>
> trigger<br>
> > > > this problem and then you can beat cray over the head with<br>
> it.<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > Sounds good, thanks.<br>
> > > ><br>
> > > ><br>
> > > > ==rob<br>
> > > ><br>
> > > > --<br>
> > > > Rob Latham<br>
> > > > Mathematics and Computer Science Division<br>
> > > > Argonne National Lab, IL USA<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > --<br>
> > > > Jim Edwards<br>
> > > ><br>
> > > > CESM Software Engineering Group<br>
> > > > National Center for Atmospheric Research<br>
> > > > Boulder, CO<br>
> > > > <a href="tel:303-497-1842" value="+13034971842">303-497-1842</a><br>
> > > ><br>
> > ><br>
> ><br>
> > --<br>
> > Rob Latham<br>
> > Mathematics and Computer Science Division<br>
> > Argonne National Lab, IL USA<br>
><br>
> --<br>
><br>
><br>
><br>
><br>
> --<br>
> Jim Edwards<br>
><br>
> CESM Software Engineering Group<br>
> National Center for Atmospheric Research<br>
> Boulder, CO<br>
> <a href="tel:303-497-1842" value="+13034971842">303-497-1842</a><br>
><br>
><br>
><br>
><br>
><br>
> --<br>
> Jim Edwards<br>
><br>
> CESM Software Engineering Group<br>
> National Center for Atmospheric Research<br>
> Boulder, CO<br>
> <a href="tel:303-497-1842" value="+13034971842">303-497-1842</a><br>
><br>
<br>
</div></div>--<br>
</blockquote></div><br><br clear="all"><br>-- <br>Jim Edwards<br><br><font>CESM Software Engineering Group<br>National Center for Atmospheric Research<br>Boulder, CO <br>303-497-1842<br></font><br>