[SOLVED] Compiling with OpenMPI fails

Question

Hello,
I am trying to compile a program (the name is iqtree) with openMPI.  Compilation without openMPI works perfectly.  However, if I try to use openMPI, I get the following error when running make:
/usr/bin/ld: cannot find -lgomp
I have extra/openmpi 1.8.4-1 installed and if I try to run ld separately, I get:
$ ld -lgomp --verbose
GNU ld (GNU Binutils) 2.25.0
Supported emulations:
elf_x86_64
elf32_x86_64
elf_i386
i386linux
elf_l1om
elf_k1om
using internal linker script:
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==================================================
attempt to open /usr/x86_64-unknown-linux-gnu/lib64/libgomp.so failed
attempt to open /usr/x86_64-unknown-linux-gnu/lib64/libgomp.a failed
attempt to open /usr/lib/libgomp.so succeeded
-lgomp (/usr/lib/libgomp.so)
libpthread.so.0 needed by /usr/lib/libgomp.so
found libpthread.so.0 at /usr/lib/libpthread.so.0
libc.so.6 needed by /usr/lib/libgomp.so
found libc.so.6 at /usr/lib/libc.so.6
ld-linux-x86-64.so.2 needed by /usr/lib/libpthread.so.0
found ld-linux-x86-64.so.2 at /usr/lib/ld-linux-x86-64.so.2
ld: warning: cannot find entry symbol _start; not setting start address
I am not sure if anything of this is relevant.  I tried to nail it down to the actual command of make that fails:
$ /usr/bin/c++ -fopenmp -O3 -g0 -static CMakeFiles/iqtree.dir/alignment.cpp.o CMakeFiles/iqtree.dir/alignmentpairwise.cpp.o CMakeFiles/iqtree.dir/circularnetwork.cpp.o CMakeFiles/iqtree.dir/eigendecomposition.cpp.o CMakeFiles/iqtree.dir/greedy.cpp.o CMakeFiles/iqtree.dir/gss.cpp.o CMakeFiles/iqtree.dir/guidedbootstrap.cpp.o CMakeFiles/iqtree.dir/gurobiwrapper.cpp.o CMakeFiles/iqtree.dir/gzstream.cpp.o CMakeFiles/iqtree.dir/hashsplitset.cpp.o CMakeFiles/iqtree.dir/iqtree.cpp.o CMakeFiles/iqtree.dir/maalignment.cpp.o CMakeFiles/iqtree.dir/matree.cpp.o CMakeFiles/iqtree.dir/mexttree.cpp.o CMakeFiles/iqtree.dir/mpdablock.cpp.o CMakeFiles/iqtree.dir/msetsblock.cpp.o CMakeFiles/iqtree.dir/msplitsblock.cpp.o CMakeFiles/iqtree.dir/modelsblock.cpp.o CMakeFiles/iqtree.dir/mtree.cpp.o CMakeFiles/iqtree.dir/mtreeset.cpp.o CMakeFiles/iqtree.dir/ncbitree.cpp.o CMakeFiles/iqtree.dir/ngs.cpp.o CMakeFiles/iqtree.dir/node.cpp.o CMakeFiles/iqtree.dir/optimization.cpp.o CMakeFiles/iqtree.dir/parsmultistate.cpp.o CMakeFiles/iqtree.dir/pattern.cpp.o CMakeFiles/iqtree.dir/pda.cpp.o CMakeFiles/iqtree.dir/pdnetwork.cpp.o CMakeFiles/iqtree.dir/pdtree.cpp.o CMakeFiles/iqtree.dir/pdtreeset.cpp.o CMakeFiles/iqtree.dir/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/phylonode.cpp.o CMakeFiles/iqtree.dir/phylosupertree.cpp.o CMakeFiles/iqtree.dir/phylotree.cpp.o CMakeFiles/iqtree.dir/phylotreesse.cpp.o CMakeFiles/iqtree.dir/pruning.cpp.o CMakeFiles/iqtree.dir/split.cpp.o CMakeFiles/iqtree.dir/splitgraph.cpp.o CMakeFiles/iqtree.dir/splitset.cpp.o CMakeFiles/iqtree.dir/stoprule.cpp.o CMakeFiles/iqtree.dir/superalignment.cpp.o CMakeFiles/iqtree.dir/superalignmentpairwise.cpp.o CMakeFiles/iqtree.dir/supernode.cpp.o CMakeFiles/iqtree.dir/tinatree.cpp.o CMakeFiles/iqtree.dir/tools.cpp.o CMakeFiles/iqtree.dir/whtest_wrapper.cpp.o CMakeFiles/iqtree.dir/lpwrapper.c.o CMakeFiles/iqtree.dir/pllnni.cpp.o CMakeFiles/iqtree.dir/phylosupertreeplen.cpp.o CMakeFiles/iqtree.dir/phylotesting.cpp.o CMakeFiles/iqtree.dir/ecopd.cpp.o CMakeFiles/iqtree.dir/ecopdmtreeset.cpp.o CMakeFiles/iqtree.dir/graph.cpp.o CMakeFiles/iqtree.dir/candidateset.cpp.o CMakeFiles/iqtree.dir/checkpoint.cpp.o CMakeFiles/iqtree.dir/upperbounds.cpp.o -o iqtree-omp -rdynamic pllrepo/src/libpll.a pllrepo/src/libpllavx.a ncl/libncl.a whtest/libwhtest.a zlib-1./usr/bin/ld: cannot find -lgomp
collect2: error: ld returned 1 exit status
2.7/libz.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a libavxkernel.a -lm
Do you think that my PC has some issues or could the command itself be wrong?  I wondered, why /usr/bin/c++ is used and not gcc?  Or is this part of the gcc compiler collection?
Thanks for you help.
Cheers,
Dominik
Last edited by fazky (2015-04-13 08:56:08)

Answer 1

Hi fazky,
$ /usr/bin/c++ -fopenmp -O3 -g0 -static CMakeFiles/iqtree.dir/alignment.cpp.o ...
First of all, It seems you are not using the openmpi compiler (mpic++) but c++ instead. In order to set the compiler, you have to run cmake with the following options:
cmake -DCMAKE_CXX_COMPILER:FILEPATH="/usr/bin/mpic++" -DCMAKE_C_COMPILER:FILEPATH="/usr/bin/mpicc" $sourcedir
where $sourcedir is the directory containing the file CMakeList.txt.
Secondly, your problem is caused by the use of the option '-static' because in Archlinux the use of static libraries is discouraged and almost all the official packages do not provide them (and for this reason ld is not able to find a static version of libgomp). You have to patch the file CMakeList.txt:
--- CMakeLists.txt 2015-04-08 09:46:08.789454325 +0200
+++ CMakeLists.txt 2015-04-08 09:47:37.910946974 +0200
@@ -59,7 +59,7 @@
if (WIN32)
message("Target OS : Windows")
# build as static binary to run on most machines
- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}")
SET(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
add_definitions(-DWIN32)
elseif (APPLE)
@@ -77,7 +77,7 @@
message("Target OS : Unix")
# build as static binary to run on most machines
# if (CMAKE_BUILD_TYPE STREQUAL "Release")
- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}")
# endif()
else()
# Note that IQ-TREE has NOT been tested on other platforms
edit: typo
Last edited by mauritiusdadd (2015-04-09 06:04:21)