[ccp4bb] CCP4i can NOT run
Dear friends, I have installed the latest version of CCP4i under Fedora 9 on my laptop HP Compaq 6515b (two processors). The system setup was done and the CCP4i interface can run normally. But if I submit a job, it displayes "STARTING" the job in the job window and will NOT actually run the job. Also I can NOT kill the job with its status as STARTING. I have checked my Tcl/tk is version 8.4 and the CCP4I_TCLTK environment variable is pointed to the right directory containing tclsh, bltwish and other files. Is there any suggestion on how to solve this problem? Thank you very much in advance. Best wishes, Yingjie Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86-21-54921117 Email: [EMAIL PROTECTED]
Re: [ccp4bb] CCP4i can NOT run
Hi Iain,
Thanks for your reply. The path for tclsh is "/usr/local/tcltkblt/bin/".
There are six files: bltsh, bltwish, tclsh, tclsh8.4, wish and wish8.4. The
tclsh
and wish are symbolic links for tclsh8.4 and wish8.4, respectively. For the
permission reason you mentioned, I have also tried this change:
sudo chown yjpeng:yjpeng -R /usr/local/tcltkblt
It does NOT work!
For better analysis, I paste my ccp4.setup file as following:
### THIS SECTION MUST BE EDITED #
# CCP4_MASTER is the location of the top-level directory containing
`ccp4-'
# This is usually the directory in which you ran the tar command to unpack
the
# code, and is assumed to be shared between machines at a multi-machine
site.
setenv CCP4_MASTER/home/prog/ccp4-6.0.2
setenv CCP4$CCP4_MASTER/ccp4-6.0.2
# Check for existence of CCP4_MASTER
if (! -e $CCP4_MASTER) then
echo "* WARNING **"
echo "The directory $CCP4_MASTER"
echo "(assigned to CCP4_MASTER) does not exist."
echo "The CCP4 programs will not run correctly, and any"
echo "installation attempt will have errors or will fail."
echo "* WARNING **"
endif
# CCP4_SCR: a per-user directory for run-time-generated scratch
# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
# BINSORT_SCR: a scratch directory for binsort's use; normally same as
CCP4_SCR
setenv CCP4_SCR /data/tmp
# check to see if this exists and if not try to make it
if (! -e $CCP4_SCR) mkdir $CCP4_SCR
if (! -e $CCP4_SCR) \
echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly."
setenv BINSORT_SCR $CCP4_SCR
### CCP4i setup - you may need to edit CCP4I_TCLTK ###
# CCP4I_TOP - the top directory of the interface
setenv CCP4I_TOP ${CCP4}/ccp4i
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
# For 'standard' installations this is /usr/local/bin
# but note the SGI distributed version of Tcl/Tk is not
# appropriate version
setenv CCP4I_TCLTK /usr/local/tcltkblt/bin
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
setenv CCP4I_HELP ${CCP4I_TOP}/help
### Optional - setting http_proxy environment
# The commented out 'setenv' line below may have to be declared to download
# and edit protein sequences using the new "Import/Edit Protein Sequences"
# (This may also be required for remote job submission in arp/warp.)
# task. If so, uncomment this line and replace the example proxy URL with
your
# relevant URL
#setenv HTTP_PROXY wwwblah.blah.ac.uk:/blah.blah
### NOVICE USERS STOP HERE #
### OPTIONS TO CUSTOMISE CCP4 #
# By default, CCP4 directories are appended to the end of paths (PATH,
# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
# to 1, then they will be prepended to the beginning of paths.
# When deciding local policy, bear in mind the possible existence of
# other CCP4 installations, and the possibility of non-CCP4 programs
# with conflicting names.
set ccp4_first_in_path = 1
# The commented-out switch statement below provides an example of how
# to use this file for several machines/architectures sharing $CCP4_MASTER.
# If necessary, uncomment and edit this. Otherwise, if you're only
supporting
# a single system alter the uncommented part as necessary.
#
# The significance of the environment variables is as follows:
# CBIN: location of the executables -- must be on your path (see below);
# CLIB: location of (binary) library files such as libccp4.a and
libccp4.so;
# MANPATH: set this if your system's `man' looks at such an environment
# variable to determine where to look for man pages. By adding
# $CCP4/man to the normal path you get the CCP4 man pages
# with keyword searching as system ones.
# MCTYPE: used for LAUE make -- see LAUE documentation
# CCP4_BROWSER: set this if you intend to use the html documentation
# (recommended). It should have the path and name of a html browser eg
# /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be
# started with the alias ccp4help and will open the file
# $CHTML/INDEX.html.
# switch (`hostname`)# edit this switch statement if used
# # for multiple systems
# case 'foo':
setenv CBIN $CCP4/bin
setenv CLIB $CCP4/lib
setenv CCP4_BROWSER firefox
if (${?MANPATH}) then
if ($ccp4_first_in_path) then
setenv MANPATH ${CCP4}/man:${MANPATH}
else
setenv MANPATH ${MANPATH}:${CCP4}/man
endif
else
if ($ccp4_first_in_path) then
setenv MANPATH ${CCP4}/man:/usr/share/man
else
setenv MANPATH /usr/share/man:${CCP4}/man
endif
endif
setenv MCTYP
Re: [ccp4bb] CCP4i can NOT run
On Tue, Sep 30, 2008 at 10:48:27AM +0800, Yingjie Peng wrote: > I have installed the latest version of CCP4i under Fedora 9 on my laptop > HP Compaq 6515b (two processors). The system setup was done and the CCP4i > interface can run normally. But if I submit a job, it displayes > "STARTING" the job in the job window and will NOT actually run the job. > Also I can NOT kill the job with its status as STARTING. I have seen similar behavior before. Is your /etc/hosts correct? The localhost line should look like this: 127.0.0.1 localhost Some of the CCP4 utilities act as miniature servers and bind to localhost to communicate between the GUI and the process. If this is actually the problem, you should see output in the shell that started ccp4i similar to this: ERROR running script can not connect to server port (RunNotification) SERVER_HOST localhost SERVER_PORT 4441 -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu
Re: [ccp4bb] CCP4i can NOT run
I have checked /etc/hosts, it is similar to what you say. I also tried to set it exactly the same as yours. But it did NOT work. Thanks! On Tue, Sep 30, 2008 at 10:24 PM, Ben Eisenbraun <[EMAIL PROTECTED]>wrote: > On Tue, Sep 30, 2008 at 10:48:27AM +0800, Yingjie Peng wrote: > > I have installed the latest version of CCP4i under Fedora 9 on my laptop > > HP Compaq 6515b (two processors). The system setup was done and the CCP4i > > interface can run normally. But if I submit a job, it displayes > > "STARTING" the job in the job window and will NOT actually run the job. > > Also I can NOT kill the job with its status as STARTING. > > I have seen similar behavior before. Is your /etc/hosts correct? The > localhost line should look like this: > > 127.0.0.1 localhost > > Some of the CCP4 utilities act as miniature servers and bind to localhost > to communicate between the GUI and the process. If this is actually the > problem, you should see output in the shell that started ccp4i similar > to this: > > ERROR running script can not connect to server port (RunNotification) > SERVER_HOST localhost SERVER_PORT 4441 > > -ben > > -- > Ben Eisenbraun > Structural Biology Grid Harvard Medical School > http://sbgrid.org http://hms.harvard.edu >
Re: [ccp4bb] CCP4i can NOT run
Hi Boaz,
Thanks for your suggestion. I have tried as you suggested. In my case,
CCP4_MASTER
can NOT set to be /home/prog.
The ccp4i did not launched because it can not locate the ccp4i.tcl file.
On Tue, Sep 30, 2008 at 8:53 PM, Boaz Shaanan <[EMAIL PROTECTED]> wrote:
> Your setup in ccp4.setup seems to be incorrect.
> You should have:
> setenv CCP4_MASTER/home/prog
>
> and then you would have:
>
> echo $CCP4 /home/prog/ccp4-6.0.2
>
> I don´t think your problem has anything to do with tcl setup.
>
>Boaz
>
> - Original Message -
> From: Yingjie Peng <[EMAIL PROTECTED]>
> Date: Tuesday, September 30, 2008 15:45
> Subject: Re: [ccp4bb] CCP4i can NOT run
> To: CCP4BB@JISCMAIL.AC.UK
>
> > Hi Iain,
> >
> > Thanks for your reply. The path for tclsh is
> > "/usr/local/tcltkblt/bin/".There are six files: bltsh, bltwish,
> > tclsh, tclsh8.4, wish and wish8.4. The
> > tclsh
> > and wish are symbolic links for tclsh8.4 and wish8.4,
> > respectively. For the
> > permission reason you mentioned, I have also tried this change:
> > sudo chown yjpeng:yjpeng -R /usr/local/tcltkblt
> > It does NOT work!
> >
> > For better analysis, I paste my ccp4.setup file as following:
> > ### THIS SECTION MUST BE EDITED #
> >
> > # CCP4_MASTER is the location of the top-level directory containing
> > `ccp4-'
> > # This is usually the directory in which you ran the tar command
> > to unpack
> > the
> > # code, and is assumed to be shared between machines at a multi-
> > machinesite.
> >
> > setenv CCP4_MASTER/home/prog/ccp4-6.0.2
> > setenv CCP4
> > $CCP4_MASTER/ccp4-6.0.2
> >
> > # Check for existence of CCP4_MASTER
> > if (! -e $CCP4_MASTER) then
> > echo "* WARNING
> > **"echo "The directory
> > $CCP4_MASTER"echo "(assigned to CCP4_MASTER)
> > does not exist."
> > echo "The CCP4 programs will not run
> > correctly, and any"
> > echo "installation attempt will have errors
> > or will fail."
> > echo "* WARNING
> > **"endif
> >
> > # CCP4_SCR: a per-user directory for run-time-generated scratch
> > # files. A dedicated scratch filesystem is probably better than
> > (/usr)/tmp# BINSORT_SCR: a scratch directory for binsort's use;
> > normally same as
> > CCP4_SCR
> >
> > setenv CCP4_SCR /data/tmp
> > # check to see if this exists and if not try to make it
> > if (! -e $CCP4_SCR) mkdir $CCP4_SCR
> > if (! -e $CCP4_SCR) \
> > echo "Unable to make CCP4_SCR. CCP4 progs
> > will not run correctly."
> >
> > setenv BINSORT_SCR $CCP4_SCR
> >
> > ### CCP4i setup - you may need to edit CCP4I_TCLTK ###
> > # CCP4I_TOP - the top directory of the interface
> > setenv CCP4I_TOP ${CCP4}/ccp4i
> > # CCP4I_TCLTK - directory containing tclsh,wish and bltwish
> > executables# as used in
> $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
> > # For 'standard' installations this is /usr/local/bin
> > # but note the SGI distributed version of Tcl/Tk is not
> > # appropriate version
> > setenv CCP4I_TCLTK /usr/local/tcltkblt/bin
> > # CCP4I_HELP - directory contain ccp4i help - default is
> > $CCP4I_TOP/helpsetenv CCP4I_HELP ${CCP4I_TOP}/help
>
> >
> > ### Optional - setting http_proxy environment
> > # The commented out 'setenv' line below may have to be declared
> > to download
> > # and edit protein sequences using the new "Import/Edit Protein
> > Sequences"# (This may also be required for remote job submission
> > in arp/warp.)
> > # task. If so, uncomment this line and replace the example proxy
> > URL with
> > your
> > # relevant URL
> >
> > #setenv HTTP_PROXY wwwblah.blah.ac.uk:/blah.blah
> >
> > ### NOVICE USERS STOP HERE #
> >
> > ### OPTIONS TO CUSTOMISE CCP4 #
> >
> > # By default, CCP4 directories are appended to the end of paths (PATH,
> > # LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path
> > is set
> > # to 1, then they will be prepended to the beginning of paths.
> > # When deciding local policy, bear in mind the possible
> > existence of
> > # other CCP4 installations, and the possibility of non-CCP4 program
