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Bug #414

Build Error Related to Recent GSL Fix

Added by Kyle Beauchamp over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Hi,

I suspect that Erik Marklund's recent fix to Gromacs (geminate.c, May 12) may have introduced some problems, at least with my cmake based build (64bit Ubuntu 9.04). I cannot build the current Git Gromacs due to linker errors. However, reverting to last week's version fixes my problems. The files that fail during build were modified in a patch that addresses GSL issues, so I suspect that something may still be wrong there. I'll walk through my build process to show you what is wrong.
git clone git://git.gromacs.org/gromacs.git
cd gromacs

Actually, there is one other problem--to get cmake to work, I have to comment out two lines from CMakeLists.txt:

#include(gmxTestErrorcodes)
#gmx_test_eintr(EINTR)

After this, I proceed as usual (I use the SSE flag and disable testing, but these should not be relevant):

ccmake ./
make -j4

Link dies with following:

[ 92%] Building C object src/tools/CMakeFiles/g_bar.dir/g_bar.c.o
libgmxana.a(gmx_analyze.c.o): In function `gmx_analyze':
gmx_analyze.c:(.text+0x329b): undefined reference to `init_gemParams'
gmx_analyze.c:(.text+0x3421): undefined reference to `takeAwayBallistic'
libgmxana.a(gmx_hbond.c.o): In function `do_hbac':
gmx_hbond.c:(.text+0x51ad): undefined reference to `takeAwayBallistic'
gmx_hbond.c:(.text+0x5795): undefined reference to `fitGemRecomb'
libgmxana.a(gmx_hbond.c.o): In function `gmx_hbond':
gmx_hbond.c:(.text+0xc278): undefined reference to `init_gemParams'
collect2: ld returned 1 exit status
make2: * [src/tools/g_analyze] Error 1
make1:
[src/tools/CMakeFiles/g_analyze.dir/all] Error 2
make1:
Waiting for unfinished jobs....
Linking C executable g_angle
Linking C executable g_bar
Linking C executable do_dssp
[ 92%] Built target g_angle
[ 92%] Built target g_bar
[ 92%] Built target do_dssp
make: *
[all] Error 2

The above errors suggest problems in g_analyze.c. I traced init_gemParams to the file geminate.c--which was updated in a recent revision. If I use last weeks version (9baecfb5c43ff6739fd89431be8c09c942a78e18) I am able to compile without error:

git clone git://git.gromacs.org/gromacs.git
cd gromacs
git checkout 9baecfb5c43ff6739fd89431be8c09c942a78e18
ccmake ./
(I set SSE and disable-testing)
make -j4
Continues to completion:
Linking C executable make_ndx
[100%] Built target make_ndx

Thanks

History

#1 Updated by Teemu Murtola over 9 years ago

The geminate.c file was missing from src/tools/CMakeLists.txt, excluding it from the build and causing the linker errors. Fixed this in the git master branch.

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