Re: [apbs-users] maximum memory limit inputgen

[Francois B. <ber...@ri...>]

Maybe look at the output of 'ulimit -a'
to check if some limits are too low for your use case.

On 08/06/2012 04:20 AM, M.V...@lu... wrote:
> Dear,
> I tried as well with the new version 1.4 but still get the same message.
> I installed first the binary /APBS-1.4-linux-x86_64/ (which btw doesn't
> have anymore inputgen.py?)
> I compiled and installed also the source version /APBS-1.4-source.
> /Still the same message.
> Have I downloaded the wrong files?
> So at the moment, I set the --gmemceil=2000 of inputgen.py which
> corresponds to the limit ~2G RAM for 32 build. Then I got the input file
> HB.in which suggests mg-para calculations with pdime 4 4 4. Does this
> mean I need to run apbs 4*4*4=64 times with async from 0:63 and then to
> merge it afterwards with mergedx2?
> Do you have another solution?
> With many thanks,
> Milos
>
> ------------------------------------------------------------------------
> *From:* Baker, Nathan [Nat...@pn...]
> *Sent:* Saturday, August 04, 2012 2:55 AM
> *To:* Monson, Kyle E; Vulovic, M.V. (MCB); apb...@li...
> *Cc:* apb...@go...
> *Subject:* RE: maximum memory limit inputgen
>
> Hello –
>
> We have a 64-bit build for APBS 1.4.  Have you tried that?
>
> Thanks,
>
> __________________________________________________
> *Nathan Baker*
> Pacific Northwest National Laboratory
> Tel:  +1-509-375-3997
> http://nabaker.me <http://nabaker.me/>
>
> *From:*Monson, Kyle E
> *Sent:* Friday, August 03, 2012 9:35 AM
> *To:* Baker, Nathan; M.V...@lu...; apb...@li...
> *Cc:* apb...@go...
> *Subject:* RE: maximum memory limit inputgen
>
> This can only be overcome with a 64-bit build of APBS. A 32-bit
> executable can only have a heap of about 2GB as you have seen.
>
> I’m not sure what our plans are for a 64-bit build.
>
> *From:*Baker, Nathan
> *Sent:* August 03, 2012 06:32
> *To:* M.V...@lu...; apb...@li...
> *Cc:* apb...@go...
> *Subject:* Re: [apbs-users] maximum memory limit inputgen
>
> Hello –
>
> Do you have the same problem with the new APBS 1.4?
>
> Thanks,
>
> __________________________________________________
> *Nathan Baker*
> Pacific Northwest National Laboratory
> Tel:  +1-509-375-3997
> http://nabaker.me <http://nabaker.me/>
>
> *From:*M.V...@lu... <mailto:M.V...@lu...>
> [mailto:M.V...@lu...]
> *Sent:* Friday, August 03, 2012 5:54 AM
> *To:* apb...@li...
> <mailto:apb...@li...>
> *Cc:* apb...@go... <mailto:apb...@go...>
> *Subject:* [apbs-users] maximum memory limit inputgen
>
> Dear all,
>
> I was trying to upped the maximum allowable memory used by APBS. I would
> like to calculate the potential distribution for a larger Hemoglobin
> molecule. Machine on which I am running the program has 256GB RAM memory.
>
> Unfortunately, I always get the same message:
>
> --------------------------------------
>
> Unable to allocate memory!
>
> (This often means you don't have enough memory available for this
> calculation.) FATAL ERROR: Unable to allocate enough memory for problem
> size.
>
> FATAL ERROR: You requested 2203582984 bytes of RAM.
>
> FATAL ERROR: Check that your system has that much memory.
>
> VASSERT: ASSERTION FAILURE!  filename vmem.c, line 252, (ram != ((void *)0))
>
> ----------------------------------------------------------------------
>
> This corresponds to 'only' ~2GB RAM. Could you help me to overcome this
> limitation?
>
> I first call inputgen.py that should allow me to define the maximum
> memory :~ python ~/soft/apbs-1.3-amd64/share/tools/manip/inputgen.py
> --gmemceil=100000 Hb.pqr
>
> And then as a second step I run apbs program on a newly generated  file
> Hb.in ~/soft/apbs-1.3-amd64/bin/apbs Hb.in
>
> And this still gives me the same error message above.
>
> Do you know what could be the problem? Am I doing something wrong?
>
> thanks a lot
>
> Milos
>
> Leiden University Medical Center
> Department of Molecular Cell Biology
> Section Electron Microscopy
> Postal Zone S1-P
> P.O.Box 9600
> 2300 RC Leiden
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>
>
>
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