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<div class="moz-cite-prefix">On 07/20/2017 04:19 PM, Shane Snyder
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:7a7d2fac-5f7c-640f-9b24-cb91d4ea6ad9@mcs.anl.gov">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hi Teng,<br>
<br>
First of all, I actually just got darshan 3.1.4 to properly
generate a log when using static linking. I'm not sure what was
leading to the problem I had earlier, but after reconfiguring and
rebuilding the library, it works for me now. I also confirmed the
nightly tests were working correctly -- the log files were going
to another spot that I wasn't expecting, so missed them the first
time around. You may want to try something similar -- just
rebuilding everything from scratch and trying again. I've also run
into this problem in the past whenever I was accidentally pointing
to an mpich build that defaults to using shared libraries rather
than the static ones, so that could be another thing to check. <br>
<br>
As for the error you are getting with Darshan 3.1.3, I've actually
never seen someone hit that before. That error would be due to the
libz compression functions (deflate) returning some sort of error.
Not exactly sure what could cause that, but is the application
opening a really large amount of files or something like that? I
suppose it's possible the compression routines could be running
out of memory if there is too much log data they are trying to
compress, but have never seen that happen before. If you aren't
already, it might be worth trying a test program that does very
basic I/O just to confirm that we can get Darshan working. One
that we frequently use is mpi-io-test -- there is a version of
this code in the darshan source @
darshan-test/regression/test-cases/src. You could try just
building that and running it (it doesn't take any command line
parameters) to see if that works?<br>
</blockquote>
<br>
Oh, actually I just noticed in your emails that you were using
mpi-io-test? That is pretty bizarre...<br>
<br>
What system are you running this on? A cluster? Your own personal
machine? If possible, you might try running somewhere else so we can
confirm the issue is some problem with the environment on the system
you have been using... I can't think of why the deflate routines
would fail when running something simple like mpi-io-test. But if
needed, we could probably get you a patch or something that tries to
give us more details on the libz error you are seeing. <br>
<br>
--Shane<br>
<br>
<blockquote type="cite"
cite="mid:7a7d2fac-5f7c-640f-9b24-cb91d4ea6ad9@mcs.anl.gov"> <br>
Thanks,<br>
--Shane<br>
<br>
<div class="moz-cite-prefix">On 07/20/2017 03:52 PM, Teng Wang
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CACSGo+rUgP1mddW+VXa3c0Jweff6WHh34wQg-pWBSCijssrd+A@mail.gmail.com">
<div dir="ltr">Hi Shane,
<div><br>
</div>
<div>Thanks for your help on this. I tried v3.1.3 and compiled
successfully. </div>
<div>But when I ran the application, there was no *.log
generated under the </div>
<div>log directory, and I also got a warning from the
application:</div>
<div>
<p
style="margin:0px;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
style="font-variant-ligatures:no-common-ligatures;color:rgb(175,173,36)"> </span><span
style="font-variant-ligatures:no-common-ligatures">darshan
library warning: unable to compress job data</span></p>
<p
style="margin:0px;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br>
</p>
</div>
<div>May I know how to fix this?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Teng</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jul 20, 2017 at 11:51 AM,
Shane Snyder <span dir="ltr"><<a
href="mailto:ssnyder@mcs.anl.gov" target="_blank"
moz-do-not-send="true">ssnyder@mcs.anl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Teng,<br>
<br>
Thanks for reporting this. This is a really strange
issue, but I can actually reproduce it, too. I'm going
to keep digging and see if I can find the problem. Will
keep you updated.<br>
<br>
The strange thing is that I was able to use version
3.1.4 successfully right before making the release
available (i.e., the log @ darshan-test/example-output/<wbr>mpi-io-test-x86_64-3.1.4.<wbr>darshan
was generated using version 3.1.4 with static linking).
Also strange is that our nightly testing is not catching
this issue...<br>
<br>
FYI, version 3.1.3 and earlier work fine for me if you
really need a quick resolution -- version 3.1.4 just
fixed a couple of non-critical bugs in some darshan log
parsing utilities, so there shouldn't be much
functionally different between the versions.<br>
<br>
--Shane
<div>
<div class="h5"><br>
<br>
<div class="m_6259078016213707887moz-cite-prefix">On
07/20/2017 12:43 PM, Teng Wang wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">
<p>Hi,</p>
<p><br>
</p>
<p>I'm having trouble when trying to statically
link </p>
<p>Darshan with mpich3.3 applications following
the instructions </p>
<p>here. Could you give me any suggestion on how
to fix it? </p>
<p><br>
</p>
<p><span style="text-decoration:underline"><a
href="http://www.mcs.anl.gov/research/projects/darshan/docs/darshan-runtime.html"
target="_blank" moz-do-not-send="true">http://www.mcs.anl.gov/<wbr>research/projects/darshan/<wbr>docs/darshan-runtime.html</a></span></p>
<p><br>
</p>
<p>Here is my steps:</p>
<p>1. Compile and install darshan 3.1.4</p>
<p>tar -xvzf darshan-3.1.4.tar.gz</p>
<p>cd darshan-3.1.4/darshan-runtime</p>
<p>./configure --with-mem-align=8
--with-log-path=<log directory>
--prefix=<install directory>
--with-jobid-env=PBS_JOBID --disable-cuserid
CC=mpicc</p>
<p>make</p>
<p>make install</p>
<p><br>
</p>
<p>2. Create log directory, which successfully
create the directory </p>
<p><span style="text-decoration:underline"><a
href="http://darshan-mk-log-dirs.pl/"
target="_blank" moz-do-not-send="true">darshan-mk-log-dirs.pl</a></span></p>
<p><br>
</p>
<p>3. Generate wrapper</p>
<p><span
style="text-decoration:underline;color:rgb(228,175,10)"><a
href="http://darshan-gen-cc.pl/"
target="_blank" moz-do-not-send="true">darshan-gen-cc.pl</a></span>
`which mpicc` --output mpicc.darshan</p>
<p><br>
</p>
<p>4. Compile application (mpi-io-test.c) using
mpicc.darshan</p>
<p>mpicc.darshan mpi-io-test.c -o mpi-io-test</p>
<p><br>
</p>
<p>After step 4, the following issue happened:</p>
<p>initthread.c:(.text+0xc59d): undefined
reference to `__wrap_fprintf'</p>
<p>initthread.c:(.text+0xc5bd): undefined
reference to `__wrap_fputs'</p>
<p>/global/homes/t/user/software_<wbr>install/mpich3.3a-static/lib/<wbr>libmpi.a(lib_libmpi_la-<wbr>finalize.o):
In function `MPIR_Add_finalize':</p>
<p>finalize.c:(.text+0x226e): undefined
reference to `__wrap_fputs'</p>
<p>finalize.c:(.text+0x227a): undefined
reference to `__wrap_fflush'</p>
<p>finalize.c:(.text+0x2286): undefined
reference to `__wrap_fflush'</p>
<p>/global/homes/t/user/software_<wbr>install/mpich3.3a-static/lib/<wbr>libmpi.a(lib_libmpi_la-util.o)<wbr>:
In function `MPIDI_OFI_control_handler':</p>
<p>util.c:(.text+0x17bc4): undefined reference
to `__wrap_fprintf'</p>
<p>/global/homes/t/user/software_<wbr>install/mpich3.3a-static/lib/<wbr>libmpi.a(lib_libmpi_la-ch4_<wbr>globals.o):
In function `MPID_Abort':</p>
<p>ch4_globals.c:(.text+0x38b): undefined
reference to `__wrap_fputs'</p>
<p>ch4_globals.c:(.text+0x397): undefined
reference to `__wrap_fflush'</p>
<p>ch4_globals.c:(.text+0x3a3): undefined
reference to `__wrap_fflush'</p>
<p>/tmp/ccyntLoA.o: In function `main':</p>
<p>mpi-io-test.c:(.text+0x5ae): undefined
reference to `__wrap_printf'</p>
<p>mpi-io-test.c:(.text+0x819): undefined
reference to `__wrap_printf'</p>
<p>/global/homes/t/user/software_<wbr>install/mpich3.3a-static/lib/<wbr>libmpi.a(lib_libmpi_la-<wbr>contextid.o):
In function `MPIR_Free_contextid':</p>
<p>contextid.c:(.text+0x1c3f): undefined
reference to `__wrap_fputs'</p>
<p>contextid.c:(.text+0x1c4b): undefined
reference to `__wrap_fflush'</p>
<p>contextid.c:(.text+0x1c57): undefined
reference to `__wrap_fflush'</p>
<p><br>
</p>
<p><br>
</p>
<p>mpicc.darshan -show mpi-io-test.c -o
mpi-io-test gave:</p>
<p><br>
</p>
<p>gcc -L/usr/lib64/slurmpmi
-L/global/common/cori/<wbr>software/libfabric/1.4.1/gnu/<wbr>lib
mpi-io-test.c -o mpi-io-test
-L/global/homes/t/user/<wbr>software_install/darshan/lib
-ldarshan -lz -Wl,@/global/homes/t/user/<wbr>software_install/darshan/<wbr>share/ld-opts/darshan-base-ld-<wbr>opts
-I/global/homes/t/user/<wbr>software_install/mpich3.3a-<wbr>static/include
-L/global/homes/t/user/<wbr>software_install/mpich3.3a-<wbr>static/lib
-lmpi -lpmi -lpmi -lpthread -lfabric -lrt
-lpmi -L/global/homes/t/user/<wbr>software_install/darshan/lib
-Wl,--start-group -ldarshan -ldarshan-stubs
-Wl,--end-group -lz -lrt -lpthread</p>
<p><br>
</p>
<p>The strange thing is when I do </p>
<p>nm libdarshan.a, it did show the functions
(e.g. __wrap_printf) were linked to </p>
<p>libdarshan.a. </p>
<p><br>
</p>
<p><b>0000000000002bf0 T __wrap__IO_getc</b></p>
<p><b>0000000000002d80 T __wrap__IO_putc</b></p>
<p><b>00000000000030b0 T __wrap___isoc99_fscanf</b></p>
<p><b>0000000000001990 T __wrap_fclose</b></p>
<p><b>00000000000011d0 T __wrap_fdopen</b></p>
<p><b>0000000000001810 T __wrap_fflush</b></p>
<p><b>0000000000002a60 T __wrap_fgetc</b></p>
<p><b>0000000000003690 T __wrap_fgets</b></p>
<p><b>0000000000000db0 T __wrap_fopen</b></p>
<p><b>0000000000000fc0 T __wrap_fopen64</b></p>
<p><b>00000000000026b0 T __wrap_fprintf</b></p>
<p><b>0000000000001c80 T __wrap_fputc</b></p>
<p><b>0000000000001fa0 T __wrap_fputs</b></p>
<p><b>00000000000028d0 T __wrap_fread</b></p>
<p><b>00000000000013d0 T __wrap_freopen</b></p>
<p><b>00000000000015f0 T __wrap_freopen64</b></p>
<p><b>00000000000032d0 T __wrap_fscanf</b></p>
<p><b>0000000000003920 T __wrap_fseek</b></p>
<p><b>0000000000003a30 T __wrap_fseeko</b></p>
<p><b>0000000000003b40 T __wrap_fseeko64</b></p>
<p><b>0000000000003c50 T __wrap_fsetpos</b></p>
<p><br>
</p>
<p>Thanks,</p>
<p>Teng</p>
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