java.lang.ClassNotFoundException or java.lang.NoClassDefFoundError
This usually means the class which you are trying to run was no found in the classpath. You need to add the class or .jar file which contains this class into the java *classpath**. For example, when you are runing a single java class from the command line, you need add the dot (.).
java -cp . YourSingleClass
#if runing a class from a jar file
java org.somepackage.SomeClass -cp myJarWithSomeClass.jar
PATH and CLASSPATH in Java>
The main difference between PATH and CLASSPATH is that PATH is an environment variable which is used to locate JDK binaries like “java” or “javac” command used to run java program and compile java source file. On the other hand, CLASSPATH, an environment variable is used by System or Application ClassLoader to locate and load compile Java bytecodes stored in the .class file.
Build and run eclipse java projects from the command line
A elispse project has a structure as follows:
the java codes are locate in src which contains many sub-directories. Here are some commands to building and runing an application on command line
#clean all old class
find ./bin/ -name "*.class" -type f -delete
#compile a .java file and put it in bin
javac -d bin -cp "./src/:/the/path/to/your/external/jars/*" src/test/A.java
#on some plateforme, you may need to specify the encoding
javac -encoding UTF-8 -d bin -cp "./src/:/the/path/to/your/external/jars/*" src/test/A.java
#runing A on cluster
java -Xss512m -Xms1G -Xmx16G -Djava.library.path="/full/path/to/jars/" -cp "./bin/:/full/path/to/jars/*" test.A -r ../inputFile.txt
#or run outside the source directory
java -Xss512m -Xms1G -Xmx16G -Djava.library.path="/full/path/to/jars/" -cp "./full/path/to/project/root/directory/bin/:/home/jlv/Soft/CellInTube/SoftJohn_lib/*" test.A -r ./inputFile.txt
Use Intel® MKL with Java
The intel post gives a detail description on how to use Intel MKL with Java. Here, the steps are restated with my project,
1. Create a java file with lapack dgetrf description (LAPACK.java)
Compile the LAPACK.java (locates in ./src/externalLibraries/) using the java compiler as below:
#at the root directory of the project (same with the following commands, unless otherwise stated)
javac -encoding UTF-8 -d bin src/externalLibraries/LAPACK.java
2. Generate headers files from the java class file
The header should be used in C file in the next step
javah -d ./src/externalLibraries/ -cp ./bin/ externalLibraries.LAPACK
This will produce externalLibraries_LAPACK.h under the directory ./src/externalLibraries/ .
3. Create the C file LAPACK.c
Use definition of Java_externalLibraries_LAPACK_dgetrf in header externalLibraries_LAPACK.h that was generated in step 2 to write file LAPACK.c, and put it in the same directory as the header file. Mkae sure the function name in LAPACK.c is the same as that in the header file externalLibraries_LAPACK.h .
4. Compiler the C file to generate a dynamic library
#this command should run at the directory locates the C and header file
icc -shared -fPIC -o ./liblapack.so LAPACK.c -I./ -I$JAVA_HOME/include/ -I$JAVA_HOME/include/linux/ -I$MKLROOT/include/ -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -lmkl_def -lc -ldl -qopenmp -lpthread
JAVA_HOME is the directory where you JDK is installed, this command will need jni.h and jni_md.h. MKLROOT is the install directory of intel’s MKL. A dynamic library liblapck.so is produeced, and can be linded by the Java code.