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Subject:

Re: Problem with orthogonal planes

From:

Patrick van der Wel <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Thu, 15 May 2008 12:50:10 -0400

Content-Type:

text/plain

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text/plain (78 lines)

I am not sure this matters for this particular problem, but did you try 
converting the nmrPipe 3D to a sparky format (or azara)? I could imagine 
that the nmrPipe data don't behave very well when viewed orthogonal to 
the nmrPipe 2D planes. The other two formats are supposedly 'blocked' 
and (I think) should be more suitable for such orthogonal views.

Patrick

PS. I should point out that I have not had to deal with this problem, so 
I am not speaking out of experience - but I have recently done the same 
as you are trying to do with a 3D data set, this was with a sparky 3D 
dataset (converted from nmrPipe).

Andrew Fowler wrote:
> Hi all,
>
> This is in some ways related to a problem Justin posted about last summer
> with regard to transposing XY planes to ZY planes, although in my case I
> want to keep the XY view and open another window for the ZY view to help me
> resolve degeneracies in my spectra. I didn't find an answer to the problem
> on the forum, but may have missed it.
>
> The long and short of the problem is, when I try to open a ZY window,
> Analysis essentially takes over my computer until it runs out of memory and
> crashes. Trying to create a contour file for the (2,3) dimension has the
> same problem, as does creating a new project, making a (15N,13C) window with
> 1H on the Z-axis, and then trying to open the spectrum. For what it's worth,
> the spectrum in HNCACB with moderate S/N, and the processed NMRPipe spectrum
> file is ~800 MB on disk.
>
> My gut feeling is that there is some sort of issue with contouring in this
> dimension. Even if I set the contour level up an order of magnitude relative
> to the "normal" view (which works fine) and then try to make a contour file,
> the file just keeps growing (I aborted at > 1 GB, the "normal" contour file
> is ~2.4 MB).
>
> I'm running Analysis (upgraded via the menu late last week) on a 2 GHz Core
> Duo iMac with 2 GB of RAM. It was compiled using Python 2.4.  Activity
> Monitor shows Python grabbing <99% CPU (expected during contouring and not
> problematic in and of itself), and also disturbingly shows the memory used
> by python (i.e. analysis) growing until it grabs well over 1.6 GB of real
> RAM plus virtual memory in excess of 12 GB before it finally crashes.
>
> Messages from analysis are:
>
>   
>>>> python(287) malloc: *** vm_allocate(size=1069056) failed (error code=3)
>>>>         
> python(287) malloc: *** error: can't allocate region
> python(287) malloc: *** set a breakpoint in szone_error to debug
> Drawing canvas tile ContourFile error: allocating contour memory
> python(287) malloc: *** vm_allocate(size=1069056) failed (error code=3)
> python(287) malloc: *** error: can't allocate region
> python(287) malloc: *** set a breakpoint in szone_error to debug
> Drawing canvas tile ContourFile error: getting xextended block data
> python(287) malloc: *** vm_allocate(size=1069056) failed (error code=3)
> python(287) malloc: *** error: can't allocate region
> python(287) malloc: *** set a breakpoint in szone_error to debug
> Drawing canvas tile ContourFile error: getting xextended block data
> python(287) malloc: *** vm_allocate(size=1069056) failed (error code=3)
> python(287) malloc: *** error: can't allocate region
> python(287) malloc: *** set a breakpoint in szone_error to debug
> unable to alloc 144d bytes
> /usr/local/ccpnmr/bin/analysis: line 8:   287 Abort trap
>   /sw/bin/python -i -O
>   $CCPNMR_TOP_DIR/ccpnmr1.0/python/ccpnmr/analysis/AnalysisGui.py
>   $1 $2 $3 $4 $5
>
> The final message is when the program crashed. Any suggestions/solutions
> will be greatly appreciated.
>
> Cheers,
> Andrew
>
>
>
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
>   

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