Zoe make issue associated with GCCcore/12.3.0 during snap install

Question

Zoe make issue associated with GCCcore/12.3.0 during snap install

Opened this issue a year ago · 1 comments

Hi! After having no problems installing snap on a cluster, I'm having problems installing snap in a second one, despite having identical conda environments.

My conda environment (on the first cluster, where it worked):
name: maker_env
channels:

defaults
bioconda
dependencies:
_libgcc_mutex=0.1=main
_openmp_mutex=5.1=1_gnu
_sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
binutils_impl_linux-64=2.38=h2a08ee3_1
binutils_linux-64=2.38.0=hc2dff05_0
gcc_impl_linux-64=11.2.0=h1234567_1
gcc_linux-64=11.2.0=h5c386dc_0
gxx_impl_linux-64=11.2.0=h1234567_1
gxx_linux-64=11.2.0=hc2dff05_0
kernel-headers_linux-64=3.10.0=h57e8cba_10
ld_impl_linux-64=2.38=h1181459_1
libgcc-devel_linux-64=11.2.0=h1234567_1
libgcc-ng=11.2.0=h1234567_1
libgomp=11.2.0=h1234567_1
libstdcxx-devel_linux-64=11.2.0=h1234567_1
libstdcxx-ng=11.2.0=h1234567_1
sysroot_linux-64=2.17=h57e8cba_10

When I imported the same conda environment to the second cluster I still received this issue:
~/scripts/snap$ make
make gcc
make[1]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap'
cd Zoe; make;
make[2]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make gcc
make[3]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make zoe-loop CC="gcc" CFLAGS="-O2 -Wall -Werror"
make[4]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
gcc -O2 -Wall -Werror -c -o zoeAlignment.o zoeAlignment.c
zoeAlignment.c: In function ‘zoeHSPCmpQuery’:
zoeAlignment.c:678:57: error: self-comparison always evaluates to false [-Werror=tautological-compare]
678 | else if (h1->q_start > h2->q_start && h2->q_end > h2->q_end) return 1;
| ^
zoeAlignment.c: In function ‘zoeHSPCmpSbjct’:
zoeAlignment.c:684:57: error: self-comparison always evaluates to false [-Werror=tautological-compare]
684 | else if (h1->s_start > h2->s_start && h2->s_end > h2->s_end) return 1;
| ^
cc1: all warnings being treated as errors
make[4]: *** [Makefile:110: zoeAlignment.o] Error 1
make[4]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make[3]: *** [Makefile:95: gcc] Error 2
make[3]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make[2]: *** [Makefile:58: default] Error 2
make[2]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make[1]: *** [Makefile:96: gcc] Error 2
make[1]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap'
make: *** [Makefile:58: default] Error 2

I'm using the same tarball for both installs (snap-2013-11-29.tar.gz).
When I try to follow this suggestion (sed -i 's/-Werror//g' Makefile* for both the snap and zoe makefiles) I get this error:
~/scripts/snap$ make
make gcc
make[1]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap'
cd Zoe; make;
make[2]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make gcc
make[3]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make zoe-loop CC="gcc" CFLAGS="-O2 -Wall "
make[4]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
gcc -o zoe-loop -O2 -Wall zoe-loop.o zoeAlignment.o zoeCDS.o zoeCounter.o zoeDNA.o zoeDistribution.o zoeDuration.o zoeFastaFile.o zoeFeature.o zoeFeatureFactory.o zoeFeatureTable.o zoeHMM.o zoeIsochore.o zoeMath.o zoeModel.o zoePhasePref.o zoeProtein.o zoeScanner.o zoeState.o zoeTools.o zoeTransition.o zoeTrellis.o -lm
/usr/bin/ld: zoeAlignment.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeAlignment.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeAlignment.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeCDS.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeCDS.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeCDS.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeCounter.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeCounter.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeCounter.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeDNA.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeDNA.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeDNA.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeDistribution.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeDistribution.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeDistribution.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeDuration.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeDuration.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeDuration.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeFastaFile.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeFastaFile.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeFastaFile.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeFeature.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeFeature.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeFeature.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeFeatureFactory.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeFeatureFactory.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeFeatureFactory.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeFeatureTable.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeFeatureTable.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeFeatureTable.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeHMM.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeHMM.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeHMM.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeIsochore.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeIsochore.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeIsochore.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeMath.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeMath.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeMath.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeModel.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeModel.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeModel.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoePhasePref.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoePhasePref.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoePhasePref.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeProtein.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeProtein.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeProtein.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeScanner.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeScanner.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeScanner.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeState.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeState.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeState.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeTools.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeTools.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeTools.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeTransition.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/bin/ld: zoeTransition.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeTransition.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
/usr/bin/ld: zoeTrellis.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeTrellis.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here
/usr/bin/ld: zoeTrellis.o:(.bss+0x10): multiple definition of `zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:61: zoe-loop] Error 1
make[4]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make[3]: *** [Makefile:95: gcc] Error 2
make[3]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make[2]: *** [Makefile:58: default] Error 2
make[2]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe'
make[1]: *** [Makefile:96: gcc] Error 2
make[1]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap'
make: *** [Makefile:58: default] Error 2

On the first cluster I was able to replicate the error by loading a module for OpenMPI that included several other modules (I will be using snap in maker on cluster2, eventually). When I removed the module GCCcore/12.3.0 the error was fixed. I am not familiar with C (or related languages) so I am unsure how to proceed from here. I will be contacting the administrators for cluster2 (different admins than cluster1) about which version of GCCcore is present. Do you have any suggestions on what steps to take to deal with these errors, and if there is a specific version of GCCcore that I should be using?

Thank you for your time.

Answer 1 · 2023-12-08T20:16:21.000Z

I suggest downloading SNAP from source and building it that way. It's been updated several times since the conda build. It's on my list to make a new build for conda, but I haven't done that yet. Building from source is as simple as downloading from GitHub and then typing `make` in the directory. https://github.com/KorfLab/SNAP /***********************************************\ Ian Korf Professor UC Davis Molecular & Cellular Biology and Genome Center ***@***.*** ***@***.*** \***********************************************/

…

On Dec 8, 2023, at 11:47 AM, Jade Mellor ***@***.***> wrote: Hi! After having no problems installing snap on a cluster, I'm having problems installing snap in a second one, despite having identical conda environments. My conda environment (on the first cluster, where it worked): name: maker_env channels: • defaults • bioconda dependencies: • _libgcc_mutex=0.1=main • _openmp_mutex=5.1=1_gnu • _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10 • binutils_impl_linux-64=2.38=h2a08ee3_1 • binutils_linux-64=2.38.0=hc2dff05_0 • gcc_impl_linux-64=11.2.0=h1234567_1 • gcc_linux-64=11.2.0=h5c386dc_0 • gxx_impl_linux-64=11.2.0=h1234567_1 • gxx_linux-64=11.2.0=hc2dff05_0 • kernel-headers_linux-64=3.10.0=h57e8cba_10 • ld_impl_linux-64=2.38=h1181459_1 • libgcc-devel_linux-64=11.2.0=h1234567_1 • libgcc-ng=11.2.0=h1234567_1 • libgomp=11.2.0=h1234567_1 • libstdcxx-devel_linux-64=11.2.0=h1234567_1 • libstdcxx-ng=11.2.0=h1234567_1 • sysroot_linux-64=2.17=h57e8cba_10 When I imported the same conda environment to the second cluster I still received this issue: ~/scripts/snap$ make make gcc make[1]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap' cd Zoe; make; make[2]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make gcc make[3]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make zoe-loop CC="gcc" CFLAGS="-O2 -Wall -Werror" make[4]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' gcc -O2 -Wall -Werror -c -o zoeAlignment.o zoeAlignment.c zoeAlignment.c: In function ‘zoeHSPCmpQuery’: zoeAlignment.c:678:57: error: self-comparison always evaluates to false [-Werror=tautological-compare] 678 | else if (h1->q_start > h2->q_start && h2->q_end > h2->q_end) return 1; | ^ zoeAlignment.c: In function ‘zoeHSPCmpSbjct’: zoeAlignment.c:684:57: error: self-comparison always evaluates to false [-Werror=tautological-compare] 684 | else if (h1->s_start > h2->s_start && h2->s_end > h2->s_end) return 1; | ^ cc1: all warnings being treated as errors make[4]: *** [Makefile:110: zoeAlignment.o] Error 1 make[4]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make[3]: *** [Makefile:95: gcc] Error 2 make[3]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make[2]: *** [Makefile:58: default] Error 2 make[2]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make[1]: *** [Makefile:96: gcc] Error 2 make[1]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap' make: *** [Makefile:58: default] Error 2 I'm using the same tarball for both installs (snap-2013-11-29.tar.gz). When I try to follow this suggestion (sed -i 's/-Werror//g' Makefile* for both the snap and zoe makefiles) I get this error: ~/scripts/snap$ make make gcc make[1]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap' cd Zoe; make; make[2]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make gcc make[3]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make zoe-loop CC="gcc" CFLAGS="-O2 -Wall " make[4]: Entering directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' gcc -o zoe-loop -O2 -Wall zoe-loop.o zoeAlignment.o zoeCDS.o zoeCounter.o zoeDNA.o zoeDistribution.o zoeDuration.o zoeFastaFile.o zoeFeature.o zoeFeatureFactory.o zoeFeatureTable.o zoeHMM.o zoeIsochore.o zoeMath.o zoeModel.o zoePhasePref.o zoeProtein.o zoeScanner.o zoeState.o zoeTools.o zoeTransition.o zoeTrellis.o -lm /usr/bin/ld: zoeAlignment.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeAlignment.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeAlignment.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeCDS.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeCDS.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeCDS.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeCounter.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeCounter.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeCounter.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeDNA.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeDNA.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeDNA.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeDistribution.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeDistribution.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeDistribution.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeDuration.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeDuration.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeDuration.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeFastaFile.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeFastaFile.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeFastaFile.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeFeature.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeFeature.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeFeature.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeFeatureFactory.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeFeatureFactory.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeFeatureFactory.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeFeatureTable.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeFeatureTable.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeFeatureTable.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeHMM.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeHMM.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeHMM.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeIsochore.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeIsochore.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeIsochore.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeMath.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeMath.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeMath.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeModel.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeModel.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeModel.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoePhasePref.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoePhasePref.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoePhasePref.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeProtein.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeProtein.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeProtein.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeScanner.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeScanner.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeScanner.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeState.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeState.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeState.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeTools.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeTools.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeTools.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeTransition.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeTransition.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeTransition.o:(.bss+0x10): multiple definition of zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here /usr/bin/ld: zoeTrellis.o:(.bss+0x0): multiple definition of zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here /usr/bin/ld: zoeTrellis.o:(.bss+0x8): multiple definition of zoeConstructor'; zoe-loop.o:(.bss+0x8): first defined here /usr/bin/ld: zoeTrellis.o:(.bss+0x10): multiple definition of `zoeFunction'; zoe-loop.o:(.bss+0x10): first defined here collect2: error: ld returned 1 exit status make[4]: *** [Makefile:61: zoe-loop] Error 1 make[4]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make[3]: *** [Makefile:95: gcc] Error 2 make[3]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make[2]: *** [Makefile:58: default] Error 2 make[2]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap/Zoe' make[1]: *** [Makefile:96: gcc] Error 2 make[1]: Leaving directory '/home/ad.uab.edu/jmellor/scripts/snap' make: *** [Makefile:58: default] Error 2 On the first cluster I was able to replicate the error by loading a module for OpenMPI that included several other modules (I will be using snap in maker on cluster2, eventually). When I removed the module GCCcore/12.3.0 the error was fixed. I am not familiar with C (or related languages) so I am unsure how to proceed from here. I will be contacting the administrators for cluster2 (different admins than cluster1) about which version of GCCcore is present. Do you have any suggestions on what steps to take to deal with these errors, and if there is a specific version of GCCcore that I should be using? Thank you for your time. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.