problem with the source command

Question

Hello, to install the freesurfer software I need to execute the two commands: setenv FREESURFER_HOME usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh but I get an error message for the second one telling me that the file SetUpFreeSurfer.csh does not exist even though it is in freesurfer. Thank you for sending me your responses. Linux Firefox 3.6.10

Xavstarblues · Answer

Hello Have you checked the rights on the file?  -- Thank you for reading the charter (above the forum list). Please mark your topics as resolved. Dura Lex, Sed Lex

dihia · Answer

Hi, thank you for your response. Yes, I checked by running the command ls -l -t and here is what it shows me: -rwxr-xr-x 1 root root 1394 2011-12-30 14:48 SetUpFreeSurfer.csh

zipe31 · Answer

Hello,  setenv FREESURFER_HOME usr/local/freesurfer  Isn't there a slash missing in front?  setenv FREESURFER_HOME /usr/local/freesurfer  -- Zen my nuggets ;-) Do something for the environment, close your windows and adopt a penguin.

dihia · Answer

@Xavstarblues: I executed the command and here's what it returns to me: /root> chmod 777 SetUpFreeSurfer.csh chmod: cannot access 'SetUpFreeSurfer.csh': Permission denied   @zip31: I don't know, I copied the command from the FreeSurfer site and it's written like this on all the sites.

dihia · Answer

there's this site: http://biowulf.nih.gov/apps/freesurfer.html I can't access the freesurferwiki site to give you the link.

dihia · Answer

and now it shows me this error: % source $FREESURFER_HOME//SetUpFreeSurfer.csh /usr/local/freesurfer/SetUpFreeSurfer.csh: Too many open files.

dubcek · Answer

hello what does the command limit descriptors respond?

dihia · Answer

hello dubcek  the command responds: no such limit

dubcek · Answer

what does the command limit return

dihia · Answer

% limit cputime illimité filesize illimité datasize illimité stacksize 8192 ko coredumpsize 0 ko memoryuse illimité memorylocked 64 ko maxproc illimité openfiles 1024

dubcek · Answer

try in root limit openfiles 2048

dihia · Answer

When I run the limit command as root, it gives this: /root> limit cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited  And when I execute the command: limit openfiles 2048 the result: no such limit.

dubcek · Answer

try as root limit descriptors 2048

dihia · Answer

the response: limit: descriptors: Can't set limit (Operation not permitted)

dubcek · Answer

~/tmp/a# limit descriptors descriptors 1024 ~/tmp/a# limit descriptors 2048 ~/tmp/a# limit descriptors descriptors 2048 ~/tmp/a#

dihia · Answer

:/root> descriptors 1024 descriptors: Command not found. nassima:/root> limit descriptors descriptors 1024 :/root> limit descriptors 2048 limit: descriptors: Can't set limit (Operation not permitted)

dubcek · Answer

what is the limit ? limit -h

dihia · Answer

Hello,  the command limit descriptors 2048 worked, but when executing the command: source $FREESURFER_HOME/SetUpFreeSurfer.csh I still get the same error too many open files.

dubcek · Answer

and in bash? bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME//SetUpFreeSurfer.sh

dihia · Answer

Thank you, it worked, but I have another issue if you can help me because I now need to execute the command qdec  it shows me this error:  /usr/local/freesurfer/bin/qdec.bin: Format error for exec(). Binary file not executable.

dubcek · Answer

`file /usr/local/freesurfer/bin/qdec.bin` returns information about the file type of `qdec.bin`, and `ls -l /usr/local/freesurfer/bin/qdec.bin` provides detailed information including permissions, number of links, owner, group, size, and last modified date.

dihia · Answer

/usr/local/freesurfer/bin/qdec.bin: exécutable ELF 64 bits LSB, x86-64, version 1 (GNU/Linux), statiquement lié, épuré

:~# ls -l /usr/local/freesurfer/bin/qdec.bin
-rwxr-xr-x 1 root root 3834580 2011-05-22 15:59 /usr/local/freesurfer/bin/qdec.bin

dubcek · Answer

Is it a 64-bit Linux? uname -a getconf LONG_BIT

dihia · Answer

root@nas:~# uname -a Linux nas2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:34:50 UTC 2010 i686 GNU/Linux root@nas:~# getconf LONG_BIT 32

dubcek · Answer

64-bit executables on a 32-bit system won't work. You need to download the 32-bit version.

dihia · Answer

Good evening, thank you very much for your help, you were right, I installed Ubuntu 64 bit and I successfully installed FreeSurfer.

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