Troubleshooting

Troubleshooting

If you experience problems installing or using Discovery Studio, review the following topic for possible solutions.

Critical errors useful for troubleshooting Discovery Studio are captured in daily log files. You can locate these log files in the following default installation directories:

If you would like to expand the amount of data collected in these log files, start the application with the -diagnostics flag.

Linux systems

Problem Possible corrective action
The Discovery Studio client does not start, or jobs submitted to the server fail. Ensure that the required system libraries are installed. Discovery Studio requires that certain libraries are present on your system. While these are typically installed by default, check that the following libraries are present:
  • Standard C++ libraries for backwards compatibility (compat-libstdc++-33)
  • Utilities for managing ext2 filesystems (e2fsprogs)
  • XML parsing library (expat)
  • Font configuration and customization library (fontconfig)
  • Portable TrueType font rendering engine (freetype)
  • GNU libc libraries (glibc)
  • Shared libraries used by Kerberos 5 (krb5-libs)
  • GCC shared support library (libgcc)
  • GNU standard C++ library (libstdc++)
  • X-Window system libraries (xorg-x11-libs)
  • Mesa utility libraries for OpenGL (XFree86-Mesa-libGL/libGLU or xorg-x11-Mesa-libGL/libGL)
Opening a 3D Window in the client causes the application to close down unexpectedly. By default, Discovery Studio uses hardware-accelerated OpenGL graphics. A problem with your graphics card or installed driver may cause the application to terminate in this manner. The following information may help you resolve these difficulties:
  • Ensure that you are using a supported graphics card and have installed graphics drivers that have been certified for use with Discovery Studio. Further details can be obtained from http://www.nvidia.com and http://www.ati.com.
  • On NVIDIA systems, an issue can arise if the security module for the PAM subsystem has changed the permissions on the NVIDIA device files. Refer to the file /usr/share/doc/NVIDIA_GLX-1.0/README installed on your system, or to http://www.nvidia.com for details on how to correct this problem.
  • Disable hardware-accelerated graphics using the 3D Window Preferences. While this may resolve the problem, it will likely result in slower graphics performance.
Session management error.

If you log onto a Linux desktop as "userA", then log on "userA's" desktop as "userB" via a terminal with the command su userB, you may see this session management error:

Session management error: Authentication Rejected,
reason : None of the authentication protocols specified
are supported and host-based authentication failed

If you then run the command su - userB, this error is avoided.

Page cannot be found in help.

If you install DS 1.6 (client) with a local user account on two separate Linux machines, then access one of these machines, you should experience no problems accessing Help topics. However if the installation was done using a different folder structure on the second machine (i.e., /home/user on one and /home/user-test on the other), the networked user gets an error message saying that the page cannot be found.

Qt assistant indexes pages and stores this information in the .assistant folder. If the directory structure changes, then that information becomes obsolete.

To fix this error, delete the following folder on Linux:

~/.assistant\contentdb40.Accelrys Discovery Studio 1.6 Online Help

Parallel Simulation protocols do not use the MPI run environment variable even if it is set in the user's .cshrc file. Create a file called shrc in the share/charmm directory of your Discovery Studio installation containing the following lines: 
MPIRUN=<mpirun command>
export MPIRUN
where <mpirun command> contains the full path to the mpirun executable in your MPICH installation.

While performing a server only install on Linux, an error like the following error appears:

java.lang.UnsatisfiedLinkError:
/tmp/ismp001/libNativeExecuteCommand.so:
libstdc++.so.5: cannot open shared object
file: No such file or directory

Install the libstdc++.so.5 library, which is required by the Accelrys License Pack for backwards compatibility for WS Red Hat Enterprise Linux 4.0.

Windows systems

Problem Possible corrective action
Page cannot be found in help.

Qt assistant indexes pages and stores this information in the .assistant folder. If the directory structure changes, then that information becomes obsolete.

To fix this error, delete the following folder on Windows:

C:\Documents and Settings\<user>\.assistant\contentdb40.Accelrys Discovery Studio 1.6 Online Help

Files no longer open automatically with Discovery Studio OR Pipeline Pilot gives an error when launching DS Visualizer or Discovery Studio.

Removing Discovery Studio 1.5 or DS Visualizer 1.5 after installing Discovery Studio 1.6 or DS Visualizer 1.6 may cause the file associations to be removed.

To fix this problem, uninstall and reinstall Discovery Studio 1.6 or DS Visualizer 1.6.

Further information

Installing Discovery Studio
General system requirements and recommendations
Finding Windows system information
Installing Discovery Studio on Linux systems
Installing Discovery Studio on Windows systems
Removing Discovery Studio