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Subject:
Re: nmrPipe software on cluster
From:
jaime combariza <[log in to unmask]>
Reply To:
Research Computing Support <[log in to unmask]>, jaime combariza <[log in to unmask]>
Date:
Tue, 22 Aug 2006 09:14:45 -0400
Content-Type:
text/plain
Parts/Attachments:
text/plain (293 lines) 
Try it now. The path to init.tcl was set incorrectly in the setup file.
I have changed it and now it does not give any errors. The plot files are
in the directory you indicated. I changed rw permissions to everybody.

We'll finish the setup for NMRPIPE.


At 05:21 PM 8/21/2006, you wrote:
>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
> >
> >

Jaime E. Combariza, Ph.D.
Assistant Director Research Computing
http://www.muohio.edu/researchcomputing
Miami University
(513) 529-5080

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