memory problem in parallel running "ARMCI DASSERT fail"

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Clicked A Few Times
Threads 2
Posts 8
11:48:27 PM PDT - Thu, Nov 1st 2012
I did series of Coupled Cluster testing calculations of FH2 using two nodes connected with infiniband, with 12 cores and 48GB memory per node.
For rather small basis and tasks, such as UCCSDT/avdz and UCCSD/vtz, everything is OK, but for tasks requiring more than 500MB memory occurs the problem.

The input file is :

start fh2
scratch_dir ./tmp
memory heap 300 mb stack 300 mb global 3000 mb
geometry units au
    H       -0.466571969    0.000000000   -3.498280516
    H        0.624505061    0.000000000   -2.532671944
    F       -0.008378972    0.000000000    0.319965748
end
basis noprint
 * library cc-pvdz # or aug-cc-pvdz or others
end
SCF
  semidirect
  DOUBLET
  UHF
  THRESH 1.0e-10
  TOL2E  1.0e-10
END
TCE
  SCF
  CCSD # or CCSDT or CCSDTQ
END
TASK TCE ENERGY


When I do UCCSD/avtz calculations, the Hartree Fock part is OK, but terminated at CC as below:
            Memory Information  
            ------------------   
          Available GA space size is    9437161950 doubles
          Available MA space size is      78639421 doubles
 Maximum block size        36 doubles
 tile_dim =     35
 Block   Spin    Irrep     Size     Offset   Alpha
 -------------------------------------------------
   1    alpha     a'     5 doubles       0       1
   2    alpha     a"     1 doubles       5       2
   3    beta      a'     4 doubles       6       3
   4    beta      a"     1 doubles      10       4
   5    alpha     a'    34 doubles      11       5
   6    alpha     a'    34 doubles      45       6
   7    alpha     a"    31 doubles      79       7
   8    beta      a'    34 doubles     110       8
   9    beta      a'    35 doubles     144       9
  10    beta      a"    31 doubles     179      10
 Global array virtual files algorithm will be used
 Parallel file system coherency ......... OK
 Integral file          = ./tmp/fh2.aoints.00
 Record size in doubles =  65536        No. of integs per rec  =  43688
 Max. records in memory =     15        Max. records in file   =   2287
 No. of bits per label  =      8        No. of bits per value  =     64
 #quartets = 1.396D+05 #integrals = 8.008D+06 #direct =  0.0% #cached =100.0%
File balance: exchanges=    12  moved=    15  time=   0.0
 Fock matrix recomputed
 1-e file size   =            12706
 1-e file name   = ./tmp/fh2.f1    
 Cpu & wall time / sec            0.2            1.1
 tce_ao2e: fast2e=1
 half-transformed integrals in memory
 2-e (intermediate) file size =       279803475
 2-e (intermediate) file name = ./tmp/fh2.v2i
 Cpu & wall time / sec            1.8            2.3
 tce_mo2e: fast2e=1
 2-e integrals stored in memory
 2-e file size   =        119972997
 2-e file name   = ./tmp/fh2.v2
 Cpu & wall time / sec           10.0           10.5
 do_pt =  F
 do_lam_pt =  F
 do_cr_pt =  F
 do_lcr_pt =  F
 do_2t_pt =  F
 T1-number-of-tasks                     6
 t1 file size   =              678
 t1 file name   = ./tmp/fh2.t1
 t1 file handle =       -998
 T2-number-of-boxes                    38
 t2 file size   =           368230
 t2 file name   = ./tmp/fh2.t2
 t2 file handle =       -995
 CCSD iterations
 -----------------------------------------------------------------
 Iter          Residuum       Correlation     Cpu    Wall    V2*C2
 -----------------------------------------------------------------
0: error ival=4
(rank:0 hostname:compute-10-15.local pid:19142):ARMCI DASSERT fail. ../../ga-5-1/armci/src/devices/openib/openib.c:armci_call_data_server():2193 cond:(pdscr->status==IBV_WC_SUCCESS)
12: error ival=4
(rank:12 hostname:compute-10-1.local pid:9867):ARMCI DASSERT fail. ../../ga-5-1/armci/src/devices/openib/openib.c:armci_call_data_server():2193 cond:(pdscr->status==IBV_WC_SUCCESS)
rank 0 in job 8  i10-15_52820   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9


For UCCSDTQ/vdz calculations, it terminated at the third iteration of CC:
 2-e file size   =           386290
 2-e file name   = ./tmp/fh2.v2
 Cpu & wall time / sec            0.4            0.4
 do_pt =  F
 do_lam_pt =  F   
 do_cr_pt =  F    
 do_lcr_pt =  F   
 do_2t_pt =  F    
 T1-number-of-tasks                     6
 t1 file size   =              140      
 t1 file name   = ./tmp/fh2.t1          
 t1 file handle =       -998
 T2-number-of-boxes                    38
 t2 file size   =            14660
 t2 file name   = ./tmp/fh2.t2
 t2 file handle =       -995
 t3 file size   =          1160539
 t3 file name   = ./tmp/fh2.t3
2: WARNING:armci_set_mem_offset: offset changed 794624 to 9244672
3: WARNING:armci_set_mem_offset: offset changed 0 to 8450048
6: WARNING:armci_set_mem_offset: offset changed 794624 to 8450048 
8: WARNING:armci_set_mem_offset: offset changed 794624 to 8450048  
13: WARNING:armci_set_mem_offset: offset changed 0 to -620834816     
 t4 file size   =         78188214
 t4 file name   = ./tmp/fh2.t4             
 CCSDTQ iterations
 --------------------------------------------------------
 Iter          Residuum       Correlation     Cpu    Wall
 --------------------------------------------------------
    1   0.2682660632262  -0.1813353786615    86.8    89.1
    2   0.0920127385001  -0.1943555090903    87.5    89.9
0: error ival=4
(rank:0 hostname:compute-10-15.local pid:19656):ARMCI DASSERT fail. ../../ga-5-1/armci/src/devices/openib/openib.c:armci_call_data_server():2193 cond:(pdscr->status==IBV_WC_SUCCESS)
12: error ival=4
(rank:12 hostname:compute-10-1.local pid:10202):ARMCI DASSERT fail. ../../ga-5-1/armci/src/devices/openib/openib.c:armci_call_data_server():2193 cond:(pdscr->status==IBV_WC_SUCCESS)
application called MPI_Abort(comm=0x84000003, 1) - process 0
rank 0 in job 13  i10-15_52820   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9


If only one node was used everything is also OK. It seems that the actually available memory becomes limited if parallel with multiple nodes.
I also checked the maximum shared memory, which is nearly 36GB:
cat /proc/sys/kernel/shmmax
37976435712


The compiling setenvs are:
setenv LARGE_FILES TRUE
setenv LIB_DEFINES "-DDFLT_TOT_MEM=16777216"
setenv NWCHEM_TOP /work2/nwchem-6.1.1
setenv NWCHEM_TARGET LINUX64
setenv ENABLE_COMPONENT yes
setenv TCGRSH /usr/bin/ssh
setenv USE_MPI "y"
setenv USE_MPIF "y"
setenv USE_MPIF4 "y"
setenv MPI_LOC /work2/intel/impi/4.1.0.024/intel64
setenv MPI_LIB ${MPI_LOC}/lib
setenv MPI_INCLUDE ${MPI_LOC}/include
setenv LIBMPI "-lmpigf -lmpigi -lmpi_ilp64 -lmpi"
setenv IB_HOME /usr
setenv IB_INCLUDE $IB_HOME/include
setenv IB_LIB $IB_HOME/lib64
setenv IB_LIB_NAME "-libverbs -libumad -lpthread -lrt"
setenv ARMCI_NETWORK OPENIB
setenv PYTHONHOME /usr
setenv PYTHONVERSION 2.4
setenv USE_PYTHON64 "y"
setenv CCSDTQ yes
setenv CCSDTLR yes
setenv NWCHEM_MODULES "all python"
setenv MKLROOT /work1/soft/intel/mkl/10.1.2.024
setenv BLASOPT "-L${MKLROOT}/lib/em64t -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm"
setenv FC "ifort -i8 -I${MKLROOT}/include"
setenv CC "icc -DMKL_ILP64 -I${MKLROOT}/include"
setenv MSG_COMMS MPI



How can I deal with this error? Did anyone get the similar problem?
Any suggestions are welcome.

Forum Vet
Threads 4
Posts 779
11:17:32 AM PDT - Fri, Nov 2nd 2012
Psd,
Your calculations are likely to be crashing while creating shared memory segments.
If you set the environmental variable ARMCI_DEFAULT_SHMMAX to a value of 2048 (or larger),
you should be able to overcome this problem.
Please keep in mind that
ARMCI_DEFAULT_SHMMAX has to be greater or equal than the kernel parameter kernel.shmmax
(Root can only change kernel.shmmax, therefore you might have to ask the system
administrator to do it).
For example, if the value of kernel.shmmax is 4294967296 as in the example below,
ARMCI_DEFAULT_SHMMAX can be at most 4096 (4294967296=4096*1024*1024)

$ sysctl kernel.shmmax
kernel.shmmax = 4294967296

Cheers, Edo

Clicked A Few Times
Threads 2
Posts 8
7:20:33 AM PDT - Sat, Nov 3rd 2012
Edo,

Thanks for your advise, but this still does not work actually.

When I setenv ARMCI_DEFAULT_SHMMAX 36000, comes this warning:
incorrect ARMCI_DEFAULT_SHMMAX should be <1,8192>mb and 2^N Found=36000

and the output error is:
 2-e (intermediate) file size =       279803475
 2-e (intermediate) file name = ./tmp/fh2.v2i
14: WARNING:armci_set_mem_offset: offset changed 0 to 12124160
13: WARNING:armci_set_mem_offset: offset changed 0 to 12124160
18: WARNING:armci_set_mem_offset: offset changed 0 to 12124160
1: WARNING:armci_set_mem_offset: offset changed 0 to 12128256
2: WARNING:armci_set_mem_offset: offset changed 0 to 12124160
6: WARNING:armci_set_mem_offset: offset changed 0 to 12124160
25: WARNING:armci_set_mem_offset: offset changed 0 to 11993088
31: WARNING:armci_set_mem_offset: offset changed 67596288 to 79589376
(rank:24 hostname:compute-11-3.local pid:8753):ARMCI DASSERT fail. ../../ga-5-1/armci/sr
c/devices/openib/openib.c:armci_server_register_region():1124 cond:(memhdl->memhndl!=((v
oid *)0))
Last System Error Message from Task 24:: Cannot allocate memory
(rank:12 hostname:compute-11-4.local pid:4225):ARMCI DASSERT fail. ../../ga-5-1/armci/sr
c/devices/openib/openib.c:armci_server_register_region():1124 cond:(memhdl->memhndl!=((v
oid *)0))
Last System Error Message from Task 12:: Cannot allocate memory
(rank:0 hostname:compute-11-32.local pid:22892):ARMCI DASSERT fail. ../../ga-5-1/armci/s
rc/devices/openib/openib.c:armci_server_register_region():1124 cond:(memhdl->memhndl!=((
void *)0))
Last System Error Message from Task 0:: Cannot allocate memory
application called MPI_Abort(comm=0x84000003, 1) - process 24
application called MPI_Abort(comm=0x84000003, 1) - process 12
application called MPI_Abort(comm=0x84000003, 1) - process 0
rank 24 in job 11  i11-32_41520   caused collective abort of all ranks
  exit status of rank 24: killed by signal 9


But if I setenv ARMCI_DEFAULT_SHMMAX <= 8192, it do not run!

As a result I still haven't find the bottleneck.



Quote:Edoapra Nov 2nd 11:17 am
Psd,
Your calculations are likely to be crashing while creating shared memory segments.
If you set the environmental variable ARMCI_DEFAULT_SHMMAX to a value of 2048 (or larger),
you should be able to overcome this problem.
Please keep in mind that
ARMCI_DEFAULT_SHMMAX has to be greater or equal than the kernel parameter kernel.shmmax
(Root can only change kernel.shmmax, therefore you might have to ask the system
administrator to do it).
For example, if the value of kernel.shmmax is 4294967296 as in the example below,
ARMCI_DEFAULT_SHMMAX can be at most 4096 (4294967296=4096*1024*1024)

$ sysctl kernel.shmmax
kernel.shmmax = 4294967296

Cheers, Edo

Forum Vet
Threads 4
Posts 779
10:54:54 AM PST - Mon, Nov 5th 2012
What is the error when you set ARMCI_DEFAULT_SHMMAX=8192 ?
Thanks, Edo

Clicked A Few Times
Threads 2
Posts 8
5:48:45 PM PST - Mon, Nov 5th 2012 
 argument  1 = fh2.nw
(rank:12 hostname:compute-11-3.local pid:1523):ARMCI DASSERT fail. ../../ga-5-1/armci/src/devices/openib/openib.c:armci_server_register_region():1124 cond:(memhdl->memhndl!=((void *)0))
Last System Error Message from Task 12:: Cannot allocate memory
application called MPI_Abort(comm=0x84000003, 1) - process 12
(rank:0 hostname:compute-11-32.local pid:4764):ARMCI DASSERT fail. ../../ga-5-1/armci/src/devices/openib/openib.c:armci_server_register_region():1124 cond:(memhdl->memhndl!=((void *)0))
Last System Error Message from Task 0:: Cannot allocate memory
rank 12 in job 2  i11-32_41208   caused collective abort of all ranks
  exit status of rank 12: killed by signal 9 
[5:i11-32] unexpected disconnect completion event from [12:i11-3]
Assertion failed in file ../../dapl_conn_rc.c at line 1128: 0
internal ABORT - process 5


Thanks!


Quote:Edoapra Nov 5th 9:54 am
What is the error when you set ARMCI_DEFAULT_SHMMAX=8192 ?
Thanks, Edo

Forum Vet
Threads 4
Posts 779
10:47:17 AM PST - Tue, Nov 6th 2012
Physical Memory
Psd,
How much physical memory is available on each node and how many processors are you using on each node?

Thanks, Edo

Clicked A Few Times
Threads 2
Posts 8
7:18:13 PM PST - Tue, Nov 6th 2012
Hi Edo

There's 48G physical memory available on each node, and 12 processors are used on each node.

It is really strange that, for a medium calculation that could run with only one node, fails using two or more nodes. I don't think this break down is caused by the lack of memory, maybe some tools such as ga are not well installed, or maybe some system services are not available. It seems that the host machine can only use up to 1GB remote memory, and the ga do not make the memory sum up.


Quote:Edoapra Nov 6th 9:47 am
Psd,
How much physical memory is available on each node and how many processors are you using on each node?

Thanks, Edo

Forum Vet
Threads 4
Posts 779
3:40:19 PM PST - Wed, Nov 7th 2012
shared memory segments
Psd,
Did you check if there are shared memory segments still allocated on the nodes of your cluster?
You can do it by running the command

ipcs -a

The scripts ipcreset can be used both to display and cleanup existing shared memory segments.
You can find it in

$NWCHEM_TOP/src/tools/ga-5-1/global/testing/ipcreset

Cheers, Edo

Clicked A Few Times
Threads 2
Posts 8
12:21:14 AM PST - Thu, Nov 15th 2012
Parallel efficiency of CC tasks
Hi Edoapra!

Thanks for your help. We have found the bottleneck and fixed it, and it works well now. This is caused by the default amount of memory infiniband can register, in default it is limited to 4G.

Besides, I performed some CC calculations, and I found that it is unsatisfactory about the paralleling efficiency. For the task as below, if I use 16 cores with 1 nodes, each iteration takes 759.6s of CPU time, but when I use 128 cores with 8 nodes, it increases to 1326s to complete one iteration. Is this normal?

Thanks!

Jun Chen
2012/11/15

the input file is:
start fh2
permanent_dir .
scratch_dir ./tmp
memory heap 500 mb stack 500 mb global 9000 mb
geometry units au
    H       -0.466571969    0.000000000   -3.498280516
    H        0.624505061    0.000000000   -2.532671944
    F       -0.008378972    0.000000000    0.319965748
#   symmetry c1
end
basis noprint
 * library aug-cc-pvqz
end
SCF
  semidirect
  DOUBLET
  RHF
  THRESH 1.0d-8
  TOL2E  1.0d-8
END
TCE
  SCF
  CCSDT
  THRESH 1.0d-5
  FREEZE atomic
  DIIS 5
END
TASK TCE ENERGY




Quote:Edoapra Nov 7th 2:40 pm
Psd,
Did you check if there are shared memory segments still allocated on the nodes of your cluster?
You can do it by running the command

ipcs -a

The scripts ipcreset can be used both to display and cleanup existing shared memory segments.
You can find it in

$NWCHEM_TOP/src/tools/ga-5-1/global/testing/ipcreset

Cheers, Edo

  • Karol Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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    Send PM
Clicked A Few Times
Threads 1
Posts 30
12:52:53 PM PST - Fri, Nov 16th 2012
Hi,
I am not surprised that your CCSDT/CCSDTQ jobs are not running (or perhaps not scaling properly).
Please look at your tilesizes you are using. For unoccupied orbitals the max. tilesize is 35 which poses a huge demand on the local memory requirement and additionally provide really poor granularity.

For the CCSDT part the local memory demand is proportional to tilesize^6, so please set for the CCSDT the tilesize parameter equal to 15.

For the CCSDTQ part the local memory demand is proportional to tilesize^8, so be even more conservative with the tilesize in these runs. I guess tilesize 8 shoule be fine.

Please also modify the memory settigns. Something like this should work
memory heap 100 mb stack 1200 mb global 2500 mb

Best,
Karol


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