Question: Abyss mpi for parallel processing
0
gravatar for robinsleith
4.1 years ago by
United States
robinsleith0 wrote:

Hello,

I am having trouble getting abyss-pe to run with the np option on a cluster. We are using Ubuntu 14.04 and I have included below the configuration call and results. Note this section 

checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... yes

Thanks

Robin

Full call

./configure --with-mpi
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) mawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for ranlib... ranlib
checking for ghc... no
checking for ghc-pkg... no
./configure: line 5182: : command not found
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for std::hash<int>... no
checking for std::tr1::hash<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... yes
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... g++ -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... yes
checking tr1/functional presence... yes
checking for tr1/functional... yes
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... yes
checking google/sparse_hash_map presence... yes
checking for google/sparse_hash_map... yes
checking unordered_map usability... no
checking unordered_map presence... no
checking for unordered_map... no
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking unordered_set usability... no
checking unordered_set presence... no
checking for unordered_set... no
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking gtest/gtest.h usability... no
checking gtest/gtest.h presence... no
checking for gtest/gtest.h... no
checking for pthread_create in -lpthread... yes
checking for main in -lgtest_main... no
checking for g++ option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Misc/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating config.h
config.status: executing depfiles commands

./configure --with-mpi=/usr/include/openmpi/

abyss assembly • 2.2k views
ADD COMMENTlink modified 4.1 years ago by Shaun Jackman420 • written 4.1 years ago by robinsleith0

Can you please move the full output to a gist? Gists can be embedded in posts. The highlighted section alone can stay as part of the post, I think.

ADD REPLYlink written 4.1 years ago by RamRS20k
1
gravatar for Shaun Jackman
4.1 years ago by
Shaun Jackman420
Vancouver, Canada
Shaun Jackman420 wrote:

Which distribution of Linux are you using? Try…

./configure --with-mpi=/usr/lib/openmpi
ADD COMMENTlink written 4.1 years ago by Shaun Jackman420
0
gravatar for pld
4.1 years ago by
pld4.8k
United States
pld4.8k wrote:

Sounds like OpenMPI isn't configured correctly or abyss can't find it.

Check here:

https://groups.google.com/forum/#!topic/abyss-users/qk035O9x03c

 

ADD COMMENTlink written 4.1 years ago by pld4.8k
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