[molpro-user] gmainv1 failure
Kirk Peterson
kipeters at wsu.edu
Mon Mar 3 02:18:09 GMT 2008
Song,
I assume you've compiled molpro with I*8 integers? I would recommend
decreasing the size of the shmmax kernel parameter. This is a segment
size, not a total allowed limit.
as root:
echo '33554432' > /proc/sys/kernel/shmmax
How much swap do you have on this system? I think Linux can be fussy
if you don't have at least as much swap as you have physical memory.
-Kirk
On Mar 2, 2008, at 5:59 PM, csong wrote:
> Dear andy
>
> Thanks for your reply
>
> I have run molpro with lower memory as you suggested, and the
> details are as
> following:
>
> if memory option adopt default value
> Variable memory set to 8000000 words, buffer space 230000 words
> the calculation stops in a few minutes at HF calculation
> error in output file:
> "NOT ENOUGH MEMORY IN SUBROUTINE AOSORT.
> ERROR EXIT
> CURRENT STACK: MAIN"
>
> if memory,480,M option was used
> the calculation stops at CCSD step
> error in output file:
> "Multipassing necessary in transformation. To avoid, increase memory
> by
>
> 1167114599 words
> NPASS IN TRSOR3 3
> insufficient memory available - require 96835362 have
> 84660125
> the request was for real words
> ERROR EXIT
> CURRENT STACK: MAIN"
>
> if memory,300,M option was used
> the calculation stops at CCSD step
> error in output file:
> "Multipassing necessary in transformation. To avoid, increase memory
> by
> 1347114599 words
> NPASS IN TRSOR3 5
> insufficient memory available - require 193670724 have
> 98359007
> the request was for real words
> ERROR EXIT
> CURRENT STACK: MAIN
> "
>
> so apparently, our ccsd calculation need more memory and the memory
> option must be
> defined
> but the system have 12GB ~98304MW memory
>
> When we define more than 480MW memory for the calculation
> run molpro will give "gmainv1 failure to allocate XXXXXX" in linux
> and the outpue file show error:
> "Failure in attempting memory allocation of XXXXXX words (XXXX Mbyte)
> This error has been generated by the operating system,
> and may be the result of insufficient system memory or paging space
> In order to avoid the problem in the MOLPRO context,
> consider also reducing the requested memory through
> the MEMORY input command, or the -m command line option
> gmainv1 failure to allocate XXXXXX
>
> ERROR EXIT
> CURRENT STACK: MAIN
>
>
>
> **********************************************************************************
> *
> *******************************
> insufficient memory available - require XX
> have 0
> the request was for real words
>
> RECURSIVE CALL OF FEHLER. EMERGENCY STOP.
> FILE INFORMATION MAY BE LOST
>
> RECURSIVE CALL OF ERROR HANDLER, FILE INFORMATION MAY BE LOST
> "
>
> but when the memory for molpro set to 11GB
> the error in output file change to
> "
> GETMEM ERROR IN GETMEM iMap 1 ALLO
>
> Memory allocation map
> ---------------------
>
> FldNam VarTyp ID Length iPos
> - - - - - - - - - - - - - - - - - - - - - - - -
> IGATIM REAL 377538531 20 188769266
> IGASTAT REAL 377538573 7 188769287
> INFO REAL 377538589 1832 188769295
> HERR REAL 377542255 21 188771128
> HERW REAL 377542299 21 188771150
> TMAX REAL 377542343 3 188771172
> DDX REAL 377542351 3 188771176
> IMAP INTE 0 4851 0
>
> STACK TRACE:
>
> SEWARD 0.00 0.00
> INPUT 0.00 0.00
>
> ERROR EXIT
> CURRENT STACK: MAIN
>
> "
>
> So is this error still caused by the linux system or any unproper
> set in molpro
> parameters?
>
>
> ------------------------------
> Song
>
>> -------------------------------------------------------------
>>
>> Song,
>>
>> Can I just confirm that the program works if you don't specify a
>> limit,
>> for some simple calculation?
>>
>> Also, do you think the job will really need 500Mb of shared memory?
>> What
>> happens if you run the calculation with a lower amount?
>>
>> Best wishes,
>>
>> Andy
>>
>> csong wrote:
>>> Dear Andy,
>>> Many thanks for your quick reply.
>>> I checked the value in /proc/sys/kernel/shmmax
>>> $ more /proc/sys/kernel/shmmax
>>> 68719476736
>>>
>>> It seems to be no limit. And I change it larger in /etc/
>>> sysctl.conf,but it's also no use.
>>>
>>> Best wishes,
>>> Song
>>>
>>>> -------------------------------------------------------------
>>>> Andy May
>>>>
>>>> Song,
>>>>
>>>> I think the limit can be found in:
>>>>
>>>> /proc/sys/kernel/shmmax
>>>>
>>>> The standard limit appears to be 32 Mb.
>>>>
>>>> Best wishes,
>>>>
>>>> Andy
>>>>
>>>> csong wrote:
>>>>> Hi,
>>>>> I have a linux machine(RHEL5 system,Intel(R) Xeon(R) CPU E5335)
>>>>> with 12GB of memory and I'm trying to execute a job but I
>>>>> can't. The error message is the following:
>>>>>
>>>>> Failure in attempting memory allocation of 500230002 words (3816
>>>>> Mbyte)
>>>>> This error has been generated by the operating system,
>>>>> and may be the result of insufficient system memory or paging
>>>>> space
>>>>> In order to avoid the problem in the MOLPRO context,
>>>>> consider also reducing the requested memory through
>>>>> the MEMORY input command, or the -m command line option
>>>>> gmainv1 failure to allocate 500230002
>>>>>
>>>>> I already had done some search for similar issues and I had
>>>>> found that a possible problem is the datasize limits, but the
>>>>> problem stills even after changing these values to unlimited.
>>>>> And I had update the kernel to the latest stable
>>>>> version(2.6.24.3), but it is also no use.
>>>>> # ulimit -a
>>>>> core file size (blocks, -c) 0
>>>>> data seg size (kbytes, -d) unlimited
>>>>> max nice (-e) 0
>>>>> file size (blocks, -f) unlimited
>>>>> pending signals (-i) 106496
>>>>> max locked memory (kbytes, -l) 32
>>>>> max memory size (kbytes, -m) unlimited
>>>>> open files (-n) 1024
>>>>> pipe size (512 bytes, -p) 8
>>>>> POSIX message queues (bytes, -q) 819200
>>>>> max rt priority (-r) 0
>>>>> stack size (kbytes, -s) 8192
>>>>> cpu time (seconds, -t) unlimited
>>>>> max user processes (-u) 106496
>>>>> virtual memory (kbytes, -v) unlimited
>>>>> file locks (-x) unlimited
>>>>>
>>>>>
>>>>> Would you help me to solve it? Thanks.
>>>>>
>>>>> Song
>>>>>
>>>>>
>>>
>
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