Troubleshooting

  1. pyNEMO crashing in MacOSX (Yosemite)?
  • Downgrade the scipy package to 0.15
  1. How to make pyNEMO to work behind firewall/proxy?
  • Set the environment variable http_proxy. eg. in Linux export http_proxy=<proxy-server>:<proxy-port>
  1. Getting this error ‘Warning: Please make sure pyjnius is installed and jvm.dll/libjvm.so/libjvm.dylib is in the path’ ?
  • This error is displayed when the application cannot find the java installation on the local machine. please install a java 7.x runtime from http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html and append the path to the library in the system path. eg. on windows SET PATH=”C:\Program Files (x86)\Java\jre1.7\bin\client” on Linux in shell export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH in osx export DYLD_LIBRARY_PATH=/System/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server:$DYLD_LIBRARY_PATH