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<div class="moz-cite-prefix">Great news- I'm glad it's resolved!<br>
<br>
On 07/21/2017 04:19 PM, Teng Wang wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CACSGo+qq6WVYY+eSMC64=EMwQfpjtcKDFKTptLpfuQxruOdUxw@mail.gmail.com">
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<div dir="ltr">Hi Phil,
<div><br>
</div>
<div>Thanks for the suggestion. I solved this issue finally </div>
<div>by recompiling zlib.</div>
<div><br>
</div>
<div>Teng</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Jul 21, 2017 at 1:05 PM, Phil
Carns <span dir="ltr"><<a href="mailto:carns@mcs.anl.gov"
target="_blank" moz-do-not-send="true">carns@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">
<div class="m_-8621407278620756273moz-cite-prefix">It
might be helpful to compare the mpich configure/compile
lines between your two configurations too, in case there
is some difference in mpich libraries that is triggering
an issue.<br>
<br>
thanks,<br>
-Phil
<div>
<div class="h5"><br>
<br>
On 07/20/2017 05:35 PM, Shane Snyder wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite"> <br>
<div class="m_-8621407278620756273moz-cite-prefix">On
07/20/2017 04:19 PM, Shane Snyder wrote:<br>
</div>
<blockquote type="cite"> 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-<wbr>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"> <br>
Thanks,<br>
--Shane<br>
<br>
<div class="m_-8621407278620756273moz-cite-prefix">On
07/20/2017 03:52 PM, Teng Wang wrote:<br>
</div>
<blockquote type="cite">
<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/mp<wbr>i-io-test-x86_64-3.1.4.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="m_-8621407278620756273h5"><br>
<br>
<div
class="m_-8621407278620756273m_6259078016213707887moz-cite-prefix">On
07/20/2017 12:43 PM, Teng Wang
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div
class="m_-8621407278620756273h5">
<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/researc<wbr>h/projects/darshan/docs/<wbr>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/l<wbr>ibmpi.a(lib_libmpi_la-finalize<wbr>.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/l<wbr>ibmpi.a(lib_libmpi_la-util.o):
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/l<wbr>ibmpi.a(lib_libmpi_la-ch4_glob<wbr>als.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/l<wbr>ibmpi.a(lib_libmpi_la-contexti<wbr>d.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/software<wbr>/libfabric/1.4.1/gnu/lib
mpi-io-test.c -o mpi-io-test
-L/global/homes/t/user/softwar<wbr>e_install/darshan/lib
-ldarshan -lz
-Wl,@/global/homes/t/user/soft<wbr>ware_install/darshan/share/ld-<wbr>opts/darshan-base-ld-opts
-I/global/homes/t/user/softwar<wbr>e_install/mpich3.3a-static/<wbr>include
-L/global/homes/t/user/softwar<wbr>e_install/mpich3.3a-static/lib
-lmpi -lpmi -lpmi -lpthread
-lfabric -lrt -lpmi
-L/global/homes/t/user/softwar<wbr>e_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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