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Bug #3028

install fail on Centos 6

Added by Blaine Mooers 5 months ago. Updated 5 months ago.

Status:
Feedback wanted
Priority:
Normal
Assignee:
-
Category:
build system
Target version:
-
Affected version - extra info:
Affected version:
2019.3
Difficulty:
uncategorized
Close

Description

We are trying to install gromacs 2019-3 on Centos 6 with cmake.
We get a message to report a bug.

[100%] Linking CXX executable ../../bin/gmx
[100%] Linking CXX executable ../../bin/template
[100%] Built target template
/usr/bin/ld: BFD version 2.20.51.0.2-5.44.el6 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: error: ld returned 1 exit status
make2: * [src/programs/CMakeFiles/gmx.dir/build.make:105: bin/gmx] Error 1
make2: Deleting file 'bin/gmx'
make1: [CMakeFiles/Makefile2:5862: src/programs/CMakeFiles/gmx.dir/all] Error 2
make: * [Makefile:163: all] Error 2

FYI, here is the build script (note specifying a specific compiler path is sometimes necessary with cmake):

#!/bin/bash
  1. JJS - 20190703
    module load cmake/3.14.5
    module load anaconda/2018.12
    export OMP_NUM_THREADS=12
    cmake -DCMAKE_C_COMPILER=/act/gcc-7.2.0/bin/gcc -DCMAKE_CXX_COMPILER=/act/gcc-7.2.0/bin/g++ -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_SIMD=AVX_256 -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3/gcc -DGMX_MPI=OFF -DGMX_OPENMP=ON -DGMX_THREAD_MPI=OFF -DGMX_BUILD_MDRUN_ONLY=OFF ..
    make -j12
    make install!

Best regards.

Blaine

History

#1 Updated by Szilárd Páll 5 months ago

  • Status changed from New to Feedback wanted
  • Target version deleted (2020-infrastructure-stable)

This looks like a linker internal error, not a bug in GROMACS. I suggest to try to upgrade your build toolchain on CentOS 6 or upgrade your OS.

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