And now, here's the main content of this page:
Known Problems and Solutions
1. Environmental setup
2. Error messages
3. Linux distribution differences
Section 1: Environment setup
You must set two environment variables in order to run PyCell Studio™.
The first is CNI_ROOT, which must point to the directory where you installed PyCell Studio.
| bash: | % export CNI_ROOT=/opt/cni |
| tcsh: | % setenv CNI_ROOT /opt/cni |
Hint: You can determine what shell you are running by typing
| all: | % env |grep SHELL |
Hint: To check where CNI_ROOT is pointing after setting it type
| all: | % env | grep CNI_ROOT |
The second step is to add PyCell Studio's bin directory to your PATH.
| bash: | % export PATH=$PATH:$CNI_ROOT/bin |
| tcsh: | % setenv PATH ${PATH}:${CNI_ROOT}/bin;rehash |
To verify that you have set up the environment correctly, type:
| all: | % which cnpy |
If everything is correct this will return the location of the cnpy script (i.e. /opt/cni/bin/cnpy). If you get a message indicating cnpy was not found, the path is incorrect, and you must repeat the above steps being carefull to point CNI_ROOT to the correct location.
Note: All commands residing in the $CNI_ROOT/bin directory are scripts. When executables are needed the script will determine the appropriate platform for your machine and invoke the corresponding executable. If you find the environment set up by these scripts is incorrect, back them up and modify them freely.
Section 2: Error messages
cnpy: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory
Cause: Some Linux distributions are missing a compatibility library.
Solution: Please see the "Linux distribution differences" section of this document for specific packages needed on your system.
MyPyCellLib/PyDiffPair/layout has no block
Cause: The OA installation you are using needs cnDloPcell.plg added to the data/plugins directory
Solution: Copy cnDloPcell.plg from the quickstart directory of your distribution to the data/plugins directory of your Open Access distribution.
Section 3: Linux distribution differences
PyCell Studio is officially supported on RedHat Enterprise Linux 3 + 4. The following are notes on those platforms.
RedHat Enterprise Linux 3
No known issues.
RedHat Enterprise Linux 4
In order to install the proper libraries for release 4 of RHEL please install the most recent version of the following RPM plus any dependancies:
compat-libstdc++-33-3.2.3
Please refer to your RedHat documentation for instructions on installing RPM packages.
Other Linux distributions
Although we do not officially support other versions of Linux, users have reported success running PyCell Studio on the following Linux distributions:
Gentoo Linux 2005.1 2005.2 and 2006.1
SuSe Linux 9.2, 9.3 and 10.0
RedHat Linux 9
Fedora Core 3
Debian (unknown version)