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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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HPC Make error: ld returned 1 exit status #47

Closed dcadam closed 5 years ago

dcadam commented 5 years ago

Wondering if you can help with this error after running make on HPC raxml-ng_v0

$ make
Scanning dependencies of target raxml_module
[  3%] Building CXX object src/CMakeFiles/raxml_module.dir/Checkpoint.cpp.o
[  7%] Building CXX object src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o
[ 10%] Building CXX object src/CMakeFiles/raxml_module.dir/LoadBalancer.cpp.o
[ 14%] Building CXX object src/CMakeFiles/raxml_module.dir/MSA.cpp.o
[ 17%] Building CXX object src/CMakeFiles/raxml_module.dir/Model.cpp.o
[ 21%] Building CXX object src/CMakeFiles/raxml_module.dir/Optimizer.cpp.o
[ 25%] Building CXX object src/CMakeFiles/raxml_module.dir/Options.cpp.o
[ 28%] Building CXX object src/CMakeFiles/raxml_module.dir/ParallelContext.cpp.o
[ 32%] Building CXX object src/CMakeFiles/raxml_module.dir/PartitionAssignment.cpp.o
[ 35%] Building CXX object src/CMakeFiles/raxml_module.dir/PartitionInfo.cpp.o
[ 39%] Building CXX object src/CMakeFiles/raxml_module.dir/PartitionedMSA.cpp.o
[ 42%] Building CXX object src/CMakeFiles/raxml_module.dir/SystemTimer.cpp.o
[ 46%] Building CXX object src/CMakeFiles/raxml_module.dir/Tree.cpp.o
[ 50%] Building CXX object src/CMakeFiles/raxml_module.dir/TreeInfo.cpp.o
[ 53%] Building CXX object src/CMakeFiles/raxml_module.dir/log.cpp.o
[ 57%] Building CXX object src/CMakeFiles/raxml_module.dir/main.cpp.o
[ 60%] Building CXX object src/CMakeFiles/raxml_module.dir/sysutil.cpp.o
[ 64%] Building CXX object src/CMakeFiles/raxml_module.dir/io/NewickStream.cpp.o
[ 67%] Building CXX object src/CMakeFiles/raxml_module.dir/io/RBAStream.cpp.o
[ 71%] Building CXX object src/CMakeFiles/raxml_module.dir/io/binary_io.cpp.o
[ 75%] Building CXX object src/CMakeFiles/raxml_module.dir/io/msa_streams.cpp.o
[ 78%] Building CXX object src/CMakeFiles/raxml_module.dir/io/part_info.cpp.o
[ 82%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/BootstopCheck.cpp.o
[ 85%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/BootstrapGenerator.cpp.o
[ 89%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/BootstrapTree.cpp.o
[ 92%] Building CXX object src/CMakeFiles/raxml_module.dir/autotune/ResourceEstimator.cpp.o
[ 96%] Building CXX object src/CMakeFiles/raxml_module.dir/terraces/TerraceWrapper.cpp.o
[100%] Linking CXX executable ../../bin/raxml-ng-mpi
/usr/bin/ld: BFD version 2.20.51.0.2-5.47.el6_9.1 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
make[2]: *** [../bin/raxml-ng-mpi] Error 1
make[2]: *** Deleting file `../bin/raxml-ng-mpi'
make[1]: *** [src/CMakeFiles/raxml_module.dir/all] Error 2
make: *** [all] Error 2
amkozlov commented 5 years ago

You need a newer version of ld, sometimes it's already there and just need to be selected (e.g. module load binutils), otherwise please ask your system administrator to install it (see: https://github.com/laurenz/oracle_fdw/issues/185#issuecomment-344256801).

Finally, you always have an option to clone github repo and compile to RAxML-NG from scratch.