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<p>After investigating, it seems that the problem appears with
debian bullseyes (ie. debian testing with glibc version 2.29-3),
but not with debian buster (debian stable with glibc version
2.28-10).</p>
<p><br>
</p>
<p>To reproduce the bug, I created the attached Dockerfile:<br>
</p>
<p><br>
</p>
<p>$ cd <PATH_TO_DOCKERFILE><br>
</p>
<p>$ docker build -t bug-darshan-isoc99_fscan .</p>
<p>[...]<br>
</p>
<p>$ docker run -it bug-darshan-isoc99_fscan /bin/bash<br>
</p>
root@8da9b1d93ddd:/# cd darshan/darshan-runtime/<br>
<p>root@8da9b1d93ddd:/darshan/darshan-runtime# make</p>
<p>[...]</p>
<p>/tmp/ccfbBbgz.s: Assembler messages:<br>
/tmp/ccfbBbgz.s:7769: Error: symbol `__isoc99_fscanf' is already
defined<br>
make: *** [Makefile:143: lib/darshan-stdio.po] Error 1<br>
root@8da9b1d93ddd:/darshan/darshan-runtime# <br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>You can build a docker image running debian stable (where the
problem does not appear) by replacing <br>
</p>
<p><br>
</p>
<p>FROM debian:testing-slim<br>
with</p>
<p>FROM debian:stable<br>
</p>
<p><br>
</p>
<p>in the Dockerfile.</p>
<p><br>
</p>
<p>François</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/11/2019 18:53, Carns, Philip H.
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:SN6PR09MB31207382D24A1E8D62841B33F7770@SN6PR09MB3120.namprd09.prod.outlook.com">
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Thanks for the bug report. It looks like maybe <font size="2"><span
style="font-size:11pt">__isoc99_fscanf</span></font>() is
defined (rather than just declared) in a header on your system.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Can you tell us a little more about your laptop (what OS/version
it is, and what version of glibc it is using)?</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
thank you,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
-Phil<br>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
Darshan-users <a class="moz-txt-link-rfc2396E" href="mailto:darshan-users-bounces@lists.mcs.anl.gov"><darshan-users-bounces@lists.mcs.anl.gov></a>
on behalf of François Trahay via Darshan-users
<a class="moz-txt-link-rfc2396E" href="mailto:darshan-users@lists.mcs.anl.gov"><darshan-users@lists.mcs.anl.gov></a><br>
<b>Sent:</b> Tuesday, November 12, 2019 6:05 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>
<a class="moz-txt-link-rfc2396E" href="mailto:darshan-users@lists.mcs.anl.gov"><darshan-users@lists.mcs.anl.gov></a><br>
<b>Subject:</b> [Darshan-users] Error: symbol
`__isoc99_fscanf' is already defined</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span
style="font-size:11pt;">
<div class="PlainText">Hi,<br>
<br>
I'm having problems compiling Darshan on my laptop running
Debian buster <br>
with MPICH-3.3.<br>
<br>
Here's how I compile:<br>
<br>
$ git clone <a
href="https://xgitlab.cels.anl.gov/darshan/darshan.git"
moz-do-not-send="true">https://xgitlab.cels.anl.gov/darshan/darshan.git</a><br>
<br>
$ cd darshan/darshan-runtime<br>
<br>
$ ./configure --prefix=$PWD/install CC=mpicc
--with-mem-align=8 <br>
--with-log-path=/tmp/log_darshan --with-jobid-env=NONE<br>
<br>
$ make<br>
<br>
[...]<br>
<br>
mpicc -DDARSHAN_CONFIG_H=\"darshan-runtime-config.h\" -I .
-I. -I./../ <br>
-g -O2 -D_LARGEFILE64_SOURCE -shared -fpic -DPIC
-DDARSHAN_PRELOAD -c <br>
lib/darshan-stdio.c -o lib/darshan-stdio.po<br>
/tmp/cc6UpHUi.s: Assembler messages:<br>
/tmp/cc6UpHUi.s:7769: Error: symbol `__isoc99_fscanf' is
already defined<br>
make: *** [Makefile:143: lib/darshan-stdio.po] Error 1<br>
<br>
<br>
The preprocessed file (darshan-stdio.c) is attached. The
problem is <br>
probably due to line 585 (in the preprocessed source code)
:<br>
<br>
extern int fscanf (FILE *__restrict __stream, const char
*__restrict <br>
__format, ...) __asm__ ("" "__isoc99_fscanf")<br>
<br>
If I comment this line, the compilation succeeds.<br>
<br>
<br>
François<br>
<br>
</div>
</span></font></div>
</blockquote>
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