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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>
<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">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<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>
</div>
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