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
|
