Re: [Apbs-users] Memory allocation error

[Baker, N. <Nat...@pn...>]

Hello –

Is this 240 GB of shared memory?  If so, are you using a 64-bit executable that can address all of that memory?

Thanks,
__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnnl.gov/bios/baker.stm

From: LUQUE BUZO, DANIEL [mailto:dl...@cn...]
Sent: Thursday, June 02, 2011 11:56 PM
To: Baker, Nathan
Cc: apb...@li...
Subject: Re: [Apbs-users] Memory allocation error

Hello-

Yes, the machine has >250 Gb of memory that is much more that the 24 Gb required.

Thanks.

Dani
Quoting "Baker, Nathan":

> Hello –
>
> The more relevant number (24372.754 MB) is in the output below.  The
> 600487976 B was simply the last thing the program tried to allocate
> before it ran out of memory.  Does your machine have >24 GB of memory?
>
> Thanks,
> __________________________________________________
> Nathan Baker
> Pacific Northwest National Laboratory
> Tel:  509-375-3997
> http://kdi.pnnl.gov/bios/baker.stm
>
> From: LUQUE BUZO, DANIEL [mailto:dl...@cn...]<mailto:[mailto:dl...@cn...]>
> Sent: Thursday, June 02, 2011 11:15 AM
> To: apb...@li...<mailto:apb...@li...>
> Subject: [Apbs-users] Memory allocation error
>
> Hello,
>
> I am trying to calculate the electrostatic potential of a quite huge
> pqr file and when I try to run apbs I receive a memory allocation
> error:
>
> 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 600487976 bytes of RAM.
> FATAL ERROR: Check that your system has that much memory.
> VASSERT: ASSERTION FAILURE!  filename vmem.c, line 252, (ram != ((void *)0))
> Abort
>
> The surprising thing is that 600487976 bytes corresponds to ~572 Mb,
> that seems to be not a really hight number. In order to be sure of
> the requested memory I have ran psize.py with the pqr file with this
> result:
>
> ################# MOLECULE INFO ####################
> Number of ATOM entries = 163619
> Number of HETATM entries (ignored) = 0
> Total charge = -16.006 e
> Dimensions = 249.520 x 285.122 x 169.285 A
> Center = 36.079 x 0.000 x 76.197 A
> Lower corner = -88.681 x -142.561 x -8.446 A
> Upper corner = 160.839 x 142.561 x 160.839 A
>
> ############## GENERAL CALCULATION INFO #############
> Coarse grid dims = 424.184 x 484.707 x 287.784 A
> Fine grid dims = 269.520 x 305.122 x 189.285 A
> Num. fine grid pts. = 545 x 609 x 385
> Parallel solve required (24372.754 MB > 400.000 MB)
> Total processors required = 288
> Proc. grid = 8 x 6 x 6
> Grid pts. on each proc. = 97 x 129 x 129
> Fine mesh spacing = 0.416569 x 0.476009 x 0.295296 A
> Estimated mem. required for parallel solve = 307.880 MB/proc.
> Number of focusing operations = 3
>
> ################# ESTIMATED REQUIREMENTS ####################
> Memory per processor                   = 307.880 MB
> Grid storage requirements (ASCII)      = 42561.308 MB
>
>
> I understand that I need ~24 Gb of RAM memory to run the process. The
> surprising thing is that I am running the process in a machine with
> >250 Gb of shared memory and, thus, this requirement of 24 Gb of
> memory sound reasonable.
>
> I have tried to re-compile apbs with the maximum memory option (in
> the configure step) set to 200 Gb with the same results of memory
> allocation error.
>
> Is there any awy to fix this problem without run it in parallel mode?
>
> Kind Regards,
>
> Dani
>