我正在尝试在LAM MPI群集计算机上安装Rmpi软件包。以前我一直在编译和测试一些东西（mpi4py和小型C ++程序），所以我确定MPI本身可以工作。但是，链接库时，安装Rmpi软件包失败。
我主要怀疑是调用makefile中的gcc而不是mpicc（我试图在配置中找到要更改此行的行，但到目前为止找不到它）。
有人在LAM上安装Rmpi有经验吗，您如何管理呢？
建筑
LAM MPI（或PBS MPI（如果存在），如何检查？）。可以肯定的是，我有一个mpicpp文件，但我认为这不是所有mpi实现的共同点
R-2.15.2
Rmpi_0.6-1
CentOS版本5.5（最终版），x86_64
从R调用的命令
install.packages("Rmpi")
记录
trying URL 'http://cran.at.r-project.org/src/contrib/Rmpi_0.6-1.tar.gz'
Content type 'application/x-gzip' length 92977 bytes (90 Kb)
opened URL
==================================================
downloaded 90 Kb
* installing *source* package âRmpiâ ...
** package âRmpiâ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/g/software/linux/pack/r-2.15.2/centos-5/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/g/software/linux/pack/r-2.15.2/centos-5/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/g/software/linux/pack/r-2.15.2/centos-5/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/g/software/linux/pack/r-2.15.2/centos-5/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi -lutil -lpthread -L/g/software/linux/pack/r-2.15.2/centos-5/lib64/R/lib -lR
/usr/bin/ld: skipping incompatible /usr/lib/libutil.so when searching for -lutil
/usr/bin/ld: skipping incompatible /usr/lib/libutil.a when searching for -lutil
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc
installing to /home/andrejev/R/x86_64-unknown-linux-gnu-library/2.15/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/andrejev/R/x86_64-unknown-linux-gnu-library/2.15/Rmpi/libs/Rmpi.so':
/usr/lib/libmpi.so.0: undefined symbol: _kio
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/home/andrejev/R/x86_64-unknown-linux-gnu-library/2.15/Rmpiâ
The downloaded source packages are in
â/tmp/Rtmp5qzeqp/downloaded_packagesâ
Warning message:
In install.packages("Rmpi") :
installation of package âRmpiâ had non-zero exit status
最佳答案
我们有一个非常相似的设置。我最近还没有接触过足够多的信息，无法与您的特定情况进行交流，但是我可以传递一些使我们正常运行的命令。
正如Dirk所提到的，对我们来说，第一步是要运行OpenMPI。设置完成后，您需要确保正确设置LD_LIBRARY_PATH：
export LD_LIBRARY_PATH=/opt/openmpiv2/lib/:$LD_LIBRARY_PATH
最终为我们安装了Rmpi的命令（运行上述命令并启动R之后）是：
install.packages("Rmpi", configure.args = c("--with-Rmpi-include=/opt/openmpiv2/include/", "--with-Rmpi-libpath=/opt/openmpiv2/lib/", "--with-Rmpi-type=OPENMPI", "--with-mpi=/opt/openmpiv2/"))
哪个为我们成功安装了软件包。然后，我们可以使用以下命令运行作业：
qsub -I -l nodes=2:ppn=12
/opt/openmpiv2/bin/mpirun --hostfile $PBS_NODEFILE -n 1 R --slave -f rmpitest.R
这些命令可能对我们的设置非常特定，以至于它们可能没有用，但是希望此处的某些命令可以节省您一些时间！
正如@Sergej在下面提出的那样，一个更通用的解决方案可能是：
install.packages(
"Rmpi",
configure.args = c(
"--with-Rmpi-include=/usr/include/", # This is where LAM's mpi.h is located
"--with-Rmpi-libpath=/usr/lib/", # This is where liblam.so is located (actually as I type it mine was located in /usr/lib64/liblam.so.0, so maybe this is not needed at all)
"--with-Rmpi-type=LAM" # This says that the type is LAM (there is also OPENMPI and MPICH)
))
我们的设置：RHEL 5，Rmpi 0.5-9，OpenMPI 1.4.3。，R 2.15.0