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Ladan Mafakher

Thalassemia & Hemoglobinopathy Research Center

i installed jdk on my serever 

i want to install osprey and for this program i should install java, mpich2 and mpijava

the instruction to install osprey according to it's manual is:

OSPREY requires Java to run. MPI is required for distributed computation. To install MPI for

distrubuted computation, two programs are required: MPICH2 (http://www-unix.mcs.anl.gov/

mpi/mpich2/index.htm), and mpiJava (http://www.hpjava.org/mpiJava.html). Following the

default installation instructions for these programs should be sucient on 32-bit machines and

some 64-bit machines. On certain 64-bit machines, however, the following modied installation

instructions must be used. These instructions assume that Java, MPICH2, and mpiJava will be

installed as subdirectories in '/home/you/mpi/' (modify this path according to your preference).

Starting with version 2.0, OSPREY also implements a multithreaded version and no longer

requires MPI to run on a single machine. If you wish to use the multithreaded version exclusively,

you can ignore steps (2) and (3) below, as well as sections 3.2 and 3.2.1.

(1) Installing 64-bit Java (v. jdk 1.6.0 06). Follow the default installation instructions.

Update your path to make sure that this java version comes rst in your path:

export PATH=/home/you/mpi/jdk1.6.0 06/bin:$PATH

(2) Modifying Java. For the mpiJava installation (see below), you may need to copy the le

'jni md.h' from 'jdk1.6.0 06/include/linux/' to 'jdk1.6.0 06/include/':

cd /home/you/mpi/jdk1.6.0 06/include/linux

cp -i jni md.h ../

(3) Installing MPICH2 (v. 1.0.7). Using bash:

tar -xzf mpich2-1.0.7.tar.gz

cd mpich2-1.0.7

export CFLAGS="-fPIC"

./congure {prex=/home/you/mpi/mpich2-install {enable-sharedlibs=gcc

make

make install

8

export PATH=/home/you/mpi/mpich2-install/bin:$PATH

(4) Installing mpiJava (v. 1.2.5). Using bash:

tar -xzf mpiJava-1.2.5.tar.gz

cd mpiJava

export DEFPINS="-shared -fPIC"

export LDFLAGSIG="-shared -fPIC"

export LDFLAG="-shared -fPIC"

./congure {with-MPI=mpich

make

export LD LIBRARY PATH=$LD LIBRARY PATH:/home/you/mpi/mpiJava/lib

export CLASSPATH=$CLASSPATH:/home/you/mpi/mpiJava/lib/classes

NOTE: ./congure {with-MPI=mpich for mpiJava may generate some errors/warnings: these

can be generally discarded; if at the end of 'make' there are no errors, then the mpiJava installation

should be successful.

(6) Installing OSPREY. After Java, mpich2, and mpiJava have been successfully installed, make

sure the third-party libraries provided with OSPREY (in the lib folder) are in your classpath. They

can be added as follows, using bash:

libpath=/whatever/OSPREY/lib

export CLASSPATH=$CLASSPATH:$libpath/architecture-rules-3.0.0-M1.jar:$libpath/commons-

logging-1.1.1.jar:$libpath/colt-1.2.0.jar:$libpath/commons-math3-3.0.jar:$libpath/commons-beanutils-

1.6.jar:$libpath/jdepend-2.9.1.jar:$libpath/commons-collections-2.1.jar:$libpath/joptimizer.jar:

$libpath/commons-digester-1.6.jar:$libpath/junit-3.8.1.jar: $libpath/commons-io-1.4.jar:$libpath/log4j-

1.2.14.jar:$libpath/commons-lang-2.5.jar:$libpath/xml-apis-1.0.b2.jar

Then, choose a directory where the OSPREY software will be installed, copy all les to that

directory, and compile using:

javac *.java

Some warning statements may be output when javac is called, but these can be generally

discarded. OSPREY should now be installed and ready for use.

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Ladan Mafakher

Thalassemia & Hemoglobinopathy Research Center

hello i have a probem in mpijava installation in step of make . the error is show below

Makefile:67: update target '../../lib/libmpi.so' due to: mpi_MPI.o mpi_Comm.o mpi_Op.o mpi_Datatype.o mpi_Intracomm.o mpi_Intercomm.o mpi_Cartcomm.o mpi_Graphcomm.o mpi_Group.o mpi_Status.o mpi_Request.o mpi_Errhandler.o

rm -f ../../lib/libmpijava.so

/usr/bin/mpicc -o ../../lib/libmpijava.so \

-L/usr/lib/mpich2-install/lib mpi_MPI.o mpi_Comm.o mpi_Op.o mpi_Datatype.o mpi_Intracomm.o mpi_Intercomm.o mpi_Cartcomm.o mpi_Graphcomm.o mpi_Group.o mpi_Status.o mpi_Request.o mpi_Errhandler.o -lmpich;

/usr/bin/ld: cannot open output file ../../lib/libmpijava.so: Permission denied

collect2: error: ld returned 1 exit status

Makefile:67: recipe for target '../../lib/libmpi.so' failed

make[2]: *** [../../lib/libmpi.so] Error 1

make[2]: Leaving directory '/usr/lib/mpiJava/src/C'

Makefile:21: recipe for target 'all' failed

make[1]: *** [all] Error 2

make[1]: Leaving directory '/usr/lib/mpiJava/src'

Makefile:34: recipe for target 'all' failed

make: *** [all] Error 2

how can solve it?

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-----------------------

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