Zoe make issue associated with GCCcore/12.3.0 during snap install

[njm-data]

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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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 ofzoeMethod'; 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 ofzoeFunction'; 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 ofzoeConstructor'; 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.

[iankorf]

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.

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