java heap size error

2016-02-14T02:47:36Z

Dear forum users,

On using the java -Xmx1200m comand to run a jar file, or using the build.sh to compile to a target jar file I got the error:
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

I tried reducing the heap with the flag -mx128m or -Xmx64m to no avail.

Any idea what is happening and how would I get over this error? Many Thanks! -Victor

BTW if I omit the -mx128m flag I had this version error for java (I posted this question posted a week ago https://www.xsede.org/group/xup/forums/-/message_boards/message/1142488):
Exception in thread "main" java.lang.UnsupportedClassVersionError: edu/cmu/ark/QuestionAsker : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

java class version mismatch?

2016-02-07T16:44:54Z

Dear forum users,

I come across java 52 version problem on running my .jar file, details as follows:

login4.stampede(44)$ ./run.sh < allslidesCleaned.txt > genQall.txt
Exception in thread "main" java.lang.UnsupportedClassVersionError: edu/cmu/ark/QuestionAsker : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

Do you know how I can get around this problem?
I ran successfully locally using java 1.7 on fedora 17 .

Many Thanks!

Victor

Cannot install python power point pptx parser on stampede

2016-02-07T03:03:05Z

Hi users on this forum,

On installing python_pptx using the pip install command I was able to compile all the dependencies but could not write the lxml library due to write permission.

Not sure if I can get around this problem ? Thanks ! Best, Victor

Details of the installation log below:

login3.stampede(42)$ pip install python-pptx
Collecting python-pptx
Using cached python-pptx-0.5.8.tar.gz
Collecting lxml>=3.1.0 (from python-pptx)
Using cached lxml-3.5.0.tar.gz
Collecting Pillow>=2.6.1 (from python-pptx)
Using cached Pillow-3.1.1.tar.gz
Collecting XlsxWriter>=0.5.7 (from python-pptx)
Using cached XlsxWriter-0.8.4-py2.py3-none-any.whl
Installing collected packages: lxml, Pillow, XlsxWriter, python-pptx
Running setup.py install for lxml
Complete output from command /opt/apps/intel15/python/2.7.9/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-gq5QCD/lxml/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ttZjZK-record/install-record.txt --single-version-externally-managed --compile:
Building lxml version 3.5.0.
Building without Cython.
Using build configuration of libxslt 1.1.26
Building against libxml2/libxslt in the following directory: /usr/lib64
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/lxml
copying src/lxml/doctestcompare.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/builder.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/__init__.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/usedoctest.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/ElementInclude.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/pyclasslookup.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/sax.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/cssselect.py -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/_elementpath.py -> build/lib.linux-x86_64-2.7/lxml
creating build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/__init__.py -> build/lib.linux-x86_64-2.7/lxml/includes
creating build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/builder.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/clean.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/defs.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/__init__.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/ElementSoup.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/usedoctest.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/html5parser.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/_diffcommand.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/formfill.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/diff.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/soupparser.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/_setmixin.py -> build/lib.linux-x86_64-2.7/lxml/html
copying src/lxml/html/_html5builder.py -> build/lib.linux-x86_64-2.7/lxml/html
creating build/lib.linux-x86_64-2.7/lxml/isoschematron
copying src/lxml/isoschematron/__init__.py -> build/lib.linux-x86_64-2.7/lxml/isoschematron
copying src/lxml/lxml.etree.h -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/lxml.etree_api.h -> build/lib.linux-x86_64-2.7/lxml
copying src/lxml/includes/xslt.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/xpath.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/schematron.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/uri.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/dtdvalid.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/tree.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/xmlerror.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/htmlparser.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/relaxng.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/xmlparser.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/config.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/xinclude.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/c14n.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/etreepublic.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/xmlschema.pxd -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/etree_defs.h -> build/lib.linux-x86_64-2.7/lxml/includes
copying src/lxml/includes/lxml-version.h -> build/lib.linux-x86_64-2.7/lxml/includes
creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources
creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/rng
copying src/lxml/isoschematron/resources/rng/iso-schematron.rng -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/rng
creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl
copying src/lxml/isoschematron/resources/xsl/XSD2Schtrn.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl
copying src/lxml/isoschematron/resources/xsl/RNG2Schtrn.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl
creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_schematron_message.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_abstract_expand.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_dsdl_include.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_schematron_skeleton_for_xslt1.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_svrl_for_xslt1.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/readme.txt -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1
running build_ext
building 'lxml.etree' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/lxml
icc -fno-strict-aliasing -ipo -fPIC -mkl -O3 -fp-model strict -fomit-frame-pointer -xhost -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -Isrc/lxml/includes -I/opt/apps/intel15/python/2.7.9/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -w
icc -shared -ipo -fp-model strict -fomit-frame-pointer -xhost -lpthread -mkl build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -L/usr/lib64 -L/opt/apps/intel15/python/2.7.9/lib -lxslt -lexslt -lxml2 -lz -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/lxml/etree.so
building 'lxml.objectify' extension
icc -fno-strict-aliasing -ipo -fPIC -mkl -O3 -fp-model strict -fomit-frame-pointer -xhost -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -Isrc/lxml/includes -I/opt/apps/intel15/python/2.7.9/include/python2.7 -c src/lxml/lxml.objectify.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.objectify.o -w
icc -shared -ipo -fp-model strict -fomit-frame-pointer -xhost -lpthread -mkl build/temp.linux-x86_64-2.7/src/lxml/lxml.objectify.o -L/usr/lib64 -L/opt/apps/intel15/python/2.7.9/lib -lxslt -lexslt -lxml2 -lz -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/lxml/objectify.so
running install_lib
creating /opt/apps/intel15/python/2.7.9/lib/python2.7/site-packages/lxml
error: could not create '/opt/apps/intel15/python/2.7.9/lib/python2.7/site-packages/lxml': Permission denied

Installation of python-pptx package on xsede

2016-02-07T02:13:24Z

Dear forum,

Recently I need to use the bigger storage space of xsede to execute my project, part of which is to read in *.pptx files and segment it to sentences.

I can easily install the python package python-pptx on my linux box but not on
stampede due to write permission for the lxml library stage.

Is there a preinstalled package that can read in pptx file and output text in some language on stampede I can use?
If not how can I install the python-pptx software on stampede on my user directory only?

Many Thanks!

Best,
Vic