Intel 64 Linux Cluster Programming, Software, and Libraries FAQ

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• SoftEnv 1.6.2 system error: could not create the file: /u/ac/jdoe/.soft.cache.csh
• My environment seems to be munged ($PATH, etc.)
• Where can I find a list of Software Applications available on NCSA HPC systems?
• Where can I find out about HDF on NCSA HPC systems?
• What does it mean when the command uberftp or mssftp fails with a Invalid CRL: The available CRL has expired error message?
• I have put all needed libraries with the -L -l flags in the command line when linking my code, why do I still get "unresolved reference" errors for some subroutines from those libraries?
• When I compile my Fortran code, I got the error message: /usr/local/intel/10.0.025/lib/libifcore.a(for_init.o)(.text+0x378): In function `for__signal_handler':: relocation truncated to fit: R_X86_64_PC32 for__l_excpt_info. What does that mean?

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When I log in, I see error messages similar to the following and it can't find any commands:

   SoftEnv 1.6.2: updating your software environment, one moment...
   SoftEnv 1.6.2 system error: could not create the file:
   /u/ac/jdoe/.soft.cache.csh

Usually this is a sign that the home quota is exceeded. If you are seeing "Command not found", you'll need to temporarily use full paths to commands. rm and mv are both in /bin.

To check your disk usage:
quota -s

My environment seems to be munged ($PATH, etc.)

As the first step, try logging off and logging back on. If this doesn'thelp, try removing the SoftEnv cache files .soft.cache.csh and .soft.cache.sh files in your home directory, and logging off and logging back on. Removing the .soft file in your home directory will cause a fresh default .soft file to be created the next time you log in, which may help as well.

Where can I find a list of Software Applications available on NCSA HPC systems?

The current listing of software applications by area of science can be found on the Software on NCSA HPC Systems page. You can also browse NCSA's software repository directly.

Where can I find out about HDF on NCSA HPC systems?

HDF/HDF5 is available on all NCSA HPC systems. Use SoftEnv for information on accessing the software. Information on support is available at the HDF Support Issues page.

What does it mean when the command uberftp or mssftp fails with a "Invalid CRL: The available CRL has expired" error message?

This error is usually caused by the presences of old(expired) *.r0 files(dot R zero) in "$HOME/.globus/certificates/" directory. The full error message would look something like...


   Failed to init security context
   GSS Major Status: Authentication Failed

   GSS Minor Status Error Chain:
   globus_gsi_gssapi: SSLv3 handshake problems
   globus_gsi_callback_module: Could not verify credential
   globus_gsi_callback_module: Could not verify credential
   globus_gsi_callback_module: Invalid CRL: The available CRL has expired


To fix the issue, move or delete your "certificates" directory in "$HOME/.globus/" and then try your mssftp or uberftp command again. If you are running these commands on NCSA production resources and if the error message remains after you have moved/deleted your "certificates" directory, please notify the Consulting Group.

I have put all needed libraries with the -L -l flags in the command line when linking my code, why do I still get "unresolved reference" errors for some subroutines from those libraries?

We have observed that with static libraries (.a), it may be due to where in the link command the -L -l flags are placed, and in the case of multiple libraries, the order of the libraries. Please put the L -l flags at the end of the link command, and if you are linking to multiple libraries, put the most dependent library first and so on, then try again.

When I compile my Fortran code, I got error message: /usr/local/intel/10.0.025/lib/libifcore.a(for_init.o)(.text+0x378): In function `for__signal_handler':: relocation truncated to fit: R_X86_64_PC32 for__l_excpt_info. What does that mean?

That may be because the static allocated data or common blocks are over 2GB. Use the -shared-intel compiler option can solve the probelm.