I think NMRpipe is being a little fussy about how it expects Tcl to be
installed. Instead of /usr/local/lib/tcl8.4, it's in /usr/lib/tcl8.4 (which
is actually a link to /usr/share/tcl8.4), so the simplest solution may be to
have Robin a link in /usr/local/lib. It looks like NMRpipe includes the
init.tcl file, but it's in /software/NMRPIPE/nmrtcl/tcl8.4 and I couldn't
figure out how to add that to where the programs look for Tcl.
Dave
-----Original Message-----
From: Research Computing Support [mailto:[log in to unmask]] On
Behalf Of Theresa A Ramelot
Sent: Monday, August 21, 2006 5:21 PM
To: [log in to unmask]
Subject: Re: nmrPipe software on cluster
Thanks Jaime,
nmrPipe and nmrDraw are running correctly. However, I have a problem with
the readROI command. It's in /software/NMRPIPE/com/readROI. I get an
error about init.tcl ,tcl, and auto_path. I don't have a variable called
auto_path set on my laptop, and it works fine. The error is below:
application-specific initialization failed: Can't find a usable init.tcl
in the following directories:
/software/NMRPIPE/nmrtxt/tcl7.6 /usr/local/lib/tcl8.4
/software/NMRPIPE/nmrtxt/tcl7.6 /software/NMRPIPE/nmrtxt/tcl8.4
/software/NMRPIPE/bin/lib/tcl8.4 /software/NMRPIPE/lib/tcl8.4
/software/NMRPIPE/bin/library /software/NMRPIPE/library
/software/NMRPIPE/tcl8.4.1/library /software/tcl8.4.1/library
/usr/local/lib/tcl8.4
This probably means that Tcl wasn't installed properly.
can't read "auto_path": no such variable
while executing
"set auto_path "[split $env(TCLPATH) :] $auto_path""
(file "/software/NMRPIPE/com/readROI" line 5)
-Theresa
Note, to test the software, cd to:
/ibrixfs1/shared/mkennedy/tramelot_king_files0/4d_noesy_spectra/er317_d2o_4d
_cc_noesy_7_5_06.fid
and then type convert.com to test nmrPipe, or proj4d.com to test the
readROI. You can view the .ft2 files with nmrDraw.
> Theresa, give it a try on redhawk.
>
> To run nmrPipe (or nmrDraw)
>
>
> 1 - connect to the cluster: ssh -Y redhawk.hpc.muohio.edu -l userid
>
> note; I needed the -Y option to force trusted X11 forwarding
>
> 2 - At this point you need to use "tcsh", if you are using any other
> shell (csh is fine),
> type "tcsh" at the prompt.
>
> 3 - source the setup file:
>
> source /software/NMRPIPE/nmrpipe.setup
>
> This file should setup all variables and give you access to the
> executables and scripts.
>
> 4 - to run nmrDraw, just type it at the prompt. i do not have any
> files to test it.
>
> 5 - later we'll set it so it will run under modules, after we check
> if it runs correctly.
>
>
>
>
> At 12:48 PM 8/19/2006, you wrote:
>>Hi Jaime,
>>
>>I found this on a help page for nmrPipe:
>>
>>" You can override NMRPipe expiration by setting the following
>> environment
>> variable (you can put this in your com/nmrInit.*.com file):
>>
>> setenv NMR_CONT CORRECT
>>"
>>
>>I seem to remember that this will work.
>>
>>Frank Delaglio used to try to make sure everyone was using the most
>> recent
>>version of nmrPipe/nmrDraw by having the expiration, but now that he has
>>left NIH, I don't know if there will be new versions for a while...
>>
>>-Theresa
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> > Theresa, some bads news (more) I am getting an Expiration error when
>> > I try to run nmrDraw or nmrPipe.
>> > I'll check further to see if I can make it run.
>> >
>> >
>> >
>> > At 03:59 PM 8/18/2006, you wrote:
>> >>Sure, I put the file in ~ramelota on the cluster. I didn't get you
>> >> e-mail
>> >>for a few hours, because sometimes my webmail doesn't refresh when I
>> hit
>> >>the button. When I log back in, I get e-mail that wasn't there when I
>> >>refreshed. I don't understand why yet.
>> >>
>> >>Thanks for trying out nmrPipe. I think our computers will be here
>> next
>> >>week. I think the next thing to try out will be getting autostructure
>> to
>> >>run on the cluster. I can get you more information on this next week.
>> >>
>> >>Thanks,
>> >>
>> >>Theresa
>> >>
>> >>
>> >> > Sure we can try the version you have. Do you have a tar file? If
>> you
>> >> > could move it to
>> >> > the cluster than I can give it a try.
>> >> >
>> >> >
>> >> >
>> >> > At 10:55 AM 8/17/2006, you wrote:
>> >> >>Hi Jaime,
>> >> >>
>> >> >>I'm not sure how to get the nmrPipe software now that Frank has
>> left
>> >> NIH.
>> >> >>I have a version on my laptop that you could try. However, I could
>> >> wait
>> >> >>and try to install it on our new computers once they arrive.
>> >> Supposedly
>> >> >>they are going to be shipped out tomorrow and will take 5-7 days to
>> >> >>arrive. I wish we had waited and found a way to buy them through
>> the
>> >> >>university so we would get the linux installed right away. It is
>> >> >> probably
>> >> >>too late to cancel the order. If I had known it was going to take
>> so
>> >> >>long, we would have cancelled it already.
>> >> >>
>> >> >>So, if you would like to try the nmrPipe software on the cluster, I
>> >> can
>> >> >>give you what I have. Otherwise, I'll wait for our computers.
>> >> >>
>> >> >>-Theresa
>> >> >>
>> >> >>
>> >> >> > Sorry Theresa. it took a long time for Frank Delaglio to answer
>> my
>> >> >> > email and this is what he wrote.
>> >> >> >
>> >> >> >
>> >> >> > (Please Do Not Reply to This Message)
>> >> >> >
>> >> >> > Dear Colleague,
>> >> >> >
>> >> >> > Very sorry for any delay in this message, or any inconvenience
>> >> >> regarding
>> >> >> > your inquiry. I resigned my permanent staff position at the
>> NIH,
>> >> >> > effective
>> >> >> > April 28, 2006. I may return to the lab for a transitional
>> period,
>> >> >> and if
>> >> >> > so, I will be sending news via email.
>> >> >> >
>> >> >> > Sincerely,
>> >> >> >
>> >> >> > Frank Delaglio
>> >> >> >
>> >> >> >
>> >> >> > At 04:40 PM 8/14/2006, Theresa A Ramelot wrote:
>> >> >> >>Hi,
>> >> >> >>
>> >> >> >>Can the nmrPipe/nmrDraw software be next on the list for
>> >> installation?
>> >> >> I
>> >> >> >>need to process some data and I could do it on my linux laptop,
>> but
>> >> I
>> >> >> >>would have to move the data back and forth, and I don't have
>> much
>> >> disk
>> >> >> >>space.
>> >> >> >>
>> >> >> >>By the way, the hottip function doesn't seem to be working for
>> me.
>> >> I
>> >> >> did
>> >> >> >>hottip NMR and see nothing. The other hottips just give me the
>> >> >> original
>> >> >> >>menu, too.
>> >> >> >>
>> >> >> >>Thanks,
>> >> >> >>
>> >> >> >>Theresa
>> >> >> >>
>> >> >> >>________________________________________
>> >> >> >>Theresa Ramelot, PhD
>> >> >> >>244 Hughes Laboratory
>> >> >> >>Department of Chemistry and Biochemistry
>> >> >> >>
>> >> >> >>FedEx address:
>> >> >> >>701 E. High Street
>> >> >> >>Department of Chemistry and Biochemistry
>> >> >> >>Miami University
>> >> >> >>Oxford, OH 45056
>> >> >> >>
>> >> >> >>work phone: (513) 529-1631
>> >> >> >>fax: (513) 529-7515
>> >> >> >>__________________________________________
>> >> >> >
>> >> >> > Jaime E. Combariza, Ph.D.
>> >> >> > Assistant Director Research Computing
>> >> >> > http://www.muohio.edu/researchcomputing
>> >> >> > Miami University
>> >> >> > (513) 529-5080
>> >> >> >
>> >> >> >
>> >> >
>> >> > Jaime E. Combariza, Ph.D.
>> >> > Assistant Director Research Computing
>> >> > http://www.muohio.edu/researchcomputing
>> >> > Miami University
>> >> > (513) 529-5080
>> >> >
>> >> >
>> >>
>> >>
>> >>________________________________________
>> >>Theresa Ramelot, PhD
>> >>244 Hughes Laboratory
>> >>Department of Chemistry and Biochemistry
>> >>
>> >>FedEx address:
>> >>701 E. High Street
>> >>Department of Chemistry and Biochemistry
>> >>Miami University
>> >>Oxford, OH 45056
>> >>
>> >>work phone: (513) 529-1631
>> >>fax: (513) 529-7515
>> >>__________________________________________
>> >
>> > Jaime E. Combariza, Ph.D.
>> > Assistant Director Research Computing
>> > http://www.muohio.edu/researchcomputing
>> > Miami University
>> > (513) 529-5080
>> >
>> >
>>
>>
>>________________________________________
>>Theresa Ramelot, PhD
>>244 Hughes Laboratory
>>Department of Chemistry and Biochemistry
>>
>>FedEx address:
>>701 E. High Street
>>Department of Chemistry and Biochemistry
>>Miami University
>>Oxford, OH 45056
>>
>>work phone: (513) 529-1631
>>fax: (513) 529-7515
>>__________________________________________
>
> Jaime E. Combariza, Ph.D.
> Assistant Director Research Computing
> http://www.muohio.edu/researchcomputing
> Miami University
> (513) 529-5080
>
>
|
