Fragmentation error during installation of pbdMPI

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Xiangcheng Mi

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Jan 15, 2016, 6:50:26 PM1/15/16

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Dear all,

I tried to install pbdMPI into my cluster under CentOS 6.4. However, I encountered an fragmentation error when testing if installed package can be loaded. The installation error occurred as following. Could you help me to solve this problem? Many thanks!

Best wishes,

Xiangcheng

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* installing *source* package 鈖bdMPI?...

** package 鈖bdMPI?successfully unpacked and MD5 sums checked

checking for sed... /bin/sed

checking for mpicc... F

checking for ompi_info... F

I am here /usr and it is OpenMPI

Trying to find mpi.h ...

Found in /usr/include/openmpi-x86_64

Trying to find libmpi.so or libmpich.a ...

Found libmpi in /usr/lib64/openmpi/lib

checking for openpty in -lutil... yes

checking for main in -lpthread... yes

******************* Results of pbdMPI package configure *****************

>> TMP_INC =

>> TMP_LIB =

>> TMP_LIBNAME =

>> MPI_ROOT = /usr

>> MPITYPE = OPENMPI

>> MPI_INCLUDE_PATH = /usr/include/openmpi-x86_64

>> MPI_LIBPATH = /usr/lib64/openmpi/lib

>> MPI_LIBNAME = libmpi.so

>> MPI_LIBS = -lutil -lpthread

>> MPI_DEFS = -DMPI2

>> MPI_INCL2 =

>> MPI_LDFLAGS =

>> PKG_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI

>> PKG_LIBS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread

>> PROF_LDFLAGS =

>> ENABLE_LD_LIBRARY_PATH = no

*************************************************************************

configure: creating ./config.status

config.status: creating src/Makevars

configure: creating ./config.status

config.status: creating src/Makevars

config.status: creating R/zzz.r

** libs

echo "MPIRUN = " > Makeconf

echo "MPIEXEC = " >> Makeconf

echo "ORTERUN = " >> Makeconf

echo "TMP_INC = " >> Makeconf

echo "TMP_LIB = " >> Makeconf

echo "TMP_LIBNAME = " >> Makeconf

echo "MPI_ROOT = /usr" >> Makeconf

echo "MPITYPE = OPENMPI" >> Makeconf

echo "MPI_INCLUDE_PATH = /usr/include/openmpi-x86_64" >> Makeconf

echo "MPI_LIBPATH = /usr/lib64/openmpi/lib" >> Makeconf

echo "MPI_LIBNAME = libmpi.so" >> Makeconf

echo "MPI_LIBS = -lutil -lpthread" >> Makeconf

echo "MPI_DEFS = -DMPI2" >> Makeconf

echo "MPI_INCL2 = " >> Makeconf

echo "MPI_LDFLAGS = " >> Makeconf

echo "PKG_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI" >> Makeconf

echo "PKG_LIBS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf

echo "PROF_LDFLAGS = " >> Makeconf

echo "ENABLE_LD_LIBRARY_PATH = no" >> Makeconf

gcc -std=gnu99 -I/build/Cellar/r/3.2.2/lib64/R/include -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O3 -march=native -mtune=native -msse4 -m128bit-long-double -fomit-frame-pointer -pipe -c comm_errors.c -o comm_errors.o

gcc -std=gnu99 -shared -L/build/Cellar/r/3.2.2/lib64/R/lib -L/usr/local/lib64 -o pbdMPI.so comm_errors.o comm_sort_double.o comm_sort_integer.o pkg_dl.o pkg_tools.o spmd.o spmd_allgather.o spmd_allgatherv.o spmd_allreduce.o spmd_alltoall.o spmd_alltoallv.o spmd_bcast.o spmd_communicator.o spmd_communicator_spawn.o spmd_gather.o spmd_gatherv.o spmd_info.o spmd_recv.o spmd_reduce.o spmd_scatter.o spmd_scatterv.o spmd_send.o spmd_sendrecv.o spmd_sendrecv_replace.o spmd_tool.o spmd_utility.o spmd_wait.o zzz.o -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread -L/build/Cellar/r/3.2.2/lib64/R/lib -lR

installing via 'install.libs.R' to /home/makeping/caoke/R/x86_64-pc-linux-gnu-library/3.2/pbdMPI

** R

** demo

** inst

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

鈖bdMPI-guide.Rnw?

** testing if installed package can be loaded

sh: line 1: 10094 Segmentation fault (core dumped) '/build/Cellar/r/3.2.2/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpBBoOsK/file251c3cb5434f'

ERROR: loading failed

* removing ?home/makeping/caoke/R/x86_64-pc-linux-gnu-library/3.2/pbdMPI?

The downloaded source packages are in

?tmp/RtmpGWu9oN/downloaded_packages?

Warning message:

In install.packages("pbdMPI") :

installation of package 鈖bdMPI?had non-zero exit status

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