[Darshan-users] Error: symbol `__isoc99_fscanf' is already defined

[Snyder, Shane]

Thanks for the additional details. I'll try to reproduce this using the Docker image you provided and will see if we can find a fix for this issue.

--Shane

On 11/13/19 3:37 AM, François Trahay via Darshan-users wrote:

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).


To reproduce the bug, I created the attached Dockerfile:


$ cd <PATH_TO_DOCKERFILE>

$  docker build -t bug-darshan-isoc99_fscan .

[...]

$ docker run -it bug-darshan-isoc99_fscan /bin/bash

root at 8da9b1d93ddd:/# cd darshan/darshan-runtime/

root at 8da9b1d93ddd:/darshan/darshan-runtime# make

[...]

/tmp/ccfbBbgz.s: Assembler messages:
/tmp/ccfbBbgz.s:7769: Error: symbol `__isoc99_fscanf' is already defined
make: *** [Makefile:143: lib/darshan-stdio.po] Error 1
root at 8da9b1d93ddd:/darshan/darshan-runtime#



You can build a docker image running debian stable (where the problem does not appear) by replacing


FROM debian:testing-slim
with

FROM debian:stable


in the Dockerfile.


François



On 12/11/2019 18:53, Carns, Philip H. wrote:
Thanks for the bug report.  It looks like maybe __isoc99_fscanf() is defined (rather than just declared) in a header on your system.

Can you tell us a little more about your laptop (what OS/version it is, and what version of glibc it is using)?

thank you,
-Phil
________________________________
From: Darshan-users <darshan-users-bounces at lists.mcs.anl.gov><mailto:darshan-users-bounces at lists.mcs.anl.gov> on behalf of François Trahay via Darshan-users <darshan-users at lists.mcs.anl.gov><mailto:darshan-users at lists.mcs.anl.gov>
Sent: Tuesday, November 12, 2019 6:05 AM
To: darshan-users at lists.mcs.anl.gov<mailto:darshan-users at lists.mcs.anl.gov> <darshan-users at lists.mcs.anl.gov><mailto:darshan-users at lists.mcs.anl.gov>
Subject: [Darshan-users] Error: symbol `__isoc99_fscanf' is already defined

Hi,

I'm having problems compiling Darshan on my laptop running Debian buster
with MPICH-3.3.

Here's how I compile:

$ git clone https://xgitlab.cels.anl.gov/darshan/darshan.git

$ cd darshan/darshan-runtime

$ ./configure --prefix=$PWD/install CC=mpicc --with-mem-align=8
--with-log-path=/tmp/log_darshan --with-jobid-env=NONE

$ make

[...]

mpicc -DDARSHAN_CONFIG_H=\"darshan-runtime-config.h\" -I . -I. -I./../
-g -O2  -D_LARGEFILE64_SOURCE -shared -fpic -DPIC -DDARSHAN_PRELOAD -c
lib/darshan-stdio.c -o lib/darshan-stdio.po
/tmp/cc6UpHUi.s: Assembler messages:
/tmp/cc6UpHUi.s:7769: Error: symbol `__isoc99_fscanf' is already defined
make: *** [Makefile:143: lib/darshan-stdio.po] Error 1


The preprocessed file (darshan-stdio.c)  is attached. The problem is
probably due to line 585 (in the preprocessed source code) :

extern int fscanf (FILE *__restrict __stream, const char *__restrict
__format, ...) __asm__ ("" "__isoc99_fscanf")

If I comment this line, the compilation succeeds.


François




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