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ROMS/TOMS

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PostPosted: Tue Oct 10, 2017 3:13 am 
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Joined: Thu May 04, 2017 1:31 pm
Posts: 20
Location: south china sea institute of oceanography
I can compile roms well, but i got "forrtl: severe (41): insufficient virtual memory" when i run it.

Code:
Node # 85 (pid=   14271) is active.
forrtl: severe (41): insufficient virtual memory
Image              PC                Routine            Line        Source             
oceanG             000000000219A9B4  mod_sources_mp_al         133  mod_sources.f90
oceanG             0000000001EB9B7D  mod_arrays_                79  mod_arrays.f90
oceanG             000000000041AEDE  ocean_control_mod         120  ocean_control.f90
oceanG             0000000000419A40  MAIN__                     95  master.f90
oceanG             0000000000419846  Unknown               Unknown  Unknown
libc.so.6          0000003921A1ED1D  Unknown               Unknown  Unknown
oceanG             0000000000419739  Unknown               Unknown  Unknown


Code:
INITIAL: Configuring and initializing forward nonlinear model ...
 *******
yhrun: error: cn2531: tasks 50-51,53-55,59,61-62,66-67,69,71: Exited with exit code 41



is that a problem about my cpp option?

my cpp is

Code:
#define ANA_BSFLUX
#define ANA_BTFLUX
/*!#define ASSUMED_SHAPE
*/
#define CURVGRID
/*
#define DIFF_GRID
*/
#define DJ_GRADPS
#define DOUBLE_PRECISION
/*#define INLINE_2DIO
*/
#define KANTHA_CLAYSON
#define MASKING
#define MIX_GEO_TS
#define MIX_S_UV
/*#define MPI */
#define MY25_MIXING
/*#define NONLINEAR
*/
#define NONLIN_EOS
#define N2S2_HORAVG
/*#define POWER_LAW
*/
#define PROFILE

#define QCORRECTION
#define K_GSCHEME
#define RADIATION_2D
/*#define !RST_SINGLE*/
#define SALINITY
#define SRELAXATION
#define SOLAR_SOURCE
#define SOLVE3D
/*!#define SPLINES
*/
/*#define SPLINES_VDIFF
*/
/*!#define SPLINE_VVISC
*/
/*#define SPONGE
*/
/*#define !STOCH_OPT_WHITE*/
#define TCLIMATOLOGY
#define TCLM_NUDGING
#define TS_A4HADVECTION
#define TS_A4VADVECTION
#define TS_DIF2
/*#define TS_PSOURCE */
#define UV_ADV
#define UV_COR
#define UV_U3HADVECTION
#define UV_C4VADVECTION
#define UV_QDRAG
/*#define UV_PSOURCE*/
#define UV_VIS2
#define VAR_RHO_2D
#define VISC_GRID



or is it something wrong about "master.f90"?


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PostPosted: Tue Oct 10, 2017 6:46 am 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3501
Location: IMS/UAF, USA
Quote:
insufficient virtual memory
The problem is that you don't have enough memory to run the domain you specify in the ocean.in file. What did you set Lm, Mm and N to? How about the number of tracers? Any idea how much memory you have on your system?


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PostPosted: Tue Oct 10, 2017 8:28 am 
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Joined: Thu May 04, 2017 1:31 pm
Posts: 20
Location: south china sea institute of oceanography
kate wrote:
Quote:
insufficient virtual memory
The problem is that you don't have enough memory to run the domain you specify in the ocean.in file. What did you set Lm, Mm and N to? How about the number of tracers? Any idea how much memory you have on your system?

thanks a lot for ur reply.


Code:
          Lm == 199          ! Number of I-direction INTERIOR RHO-points
          Mm == 215           ! Number of J-direction INTERIOR RHO-points
           N == 30            ! Number of vertical levels

        Nbed =  0             ! Number of sediment bed layers

         NAT =  2             ! Number of active tracers (usually, 2)
         NPT =  0             ! Number of inactive passive tracers
         NCS =  0             ! Number of cohesive (mud) sediment tracers
         NNS =  0             ! Number of non-cohesive (sand) sediment tracers




Code:
      NtileI == 23                                ! I-direction partition
      NtileJ == 24                              ! J-direction partition



Linux ln1 2.6.32-431.TH.x86_64 #66 SMP Sat Jan 10 13:54:00 CST 2015 x86_64 x86_64 x86_64 GNU/Linux

Code:
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1032191
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024000
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 1024
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited


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PostPosted: Tue Oct 10, 2017 5:10 pm 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3501
Location: IMS/UAF, USA
Quote:
Lm == 199 ! Number of I-direction INTERIOR RHO-points
Mm == 215 ! Number of J-direction INTERIOR RHO-points
N == 30 ! Number of vertical levels
Nbed = 0 ! Number of sediment bed layers
NAT = 2 ! Number of active tracers (usually, 2)
This is not what I would consider to be a large domain, probably not your problem.
Quote:
NtileI == 23 ! I-direction partition
NtileJ == 24 ! J-direction partition
On the other hand, this is asking for 552 processes for a modest domain and probably is your problem. What if you ask for a total of 4-8 processes instead? How many cores are in your computer? Is this some small laptop or desktop system? Your output from the limit command only reports operating system-imposed limits, not what you actually have for memory or anything.


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PostPosted: Wed Oct 11, 2017 12:38 am 
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Joined: Thu May 04, 2017 1:31 pm
Posts: 20
Location: south china sea institute of oceanography
kate wrote:
Quote:
Lm == 199 ! Number of I-direction INTERIOR RHO-points
Mm == 215 ! Number of J-direction INTERIOR RHO-points
This is not what I would consider to be a large domain, probably not your problem.

thanks for ur reply. i run it on a super computer. It should be fine to ask for 552 processes. In order to rule out the error, I changed NtileI as 12 and NtileJ as 4( Resolution, Grid 01: 0199x0215x030, Parallel Nodes: 48, Tiling: 012x004), the same problem still exist. In order to make sure the super computer is ok, I also run a bio_toy example sucessfully in this super computer. the input files (frc,ini,bry,runoff and so on) and study area are same. but cpp option is different. the two models can compile sucessfully. however, this one (adding some dynamical cpp options) can not run sucessfully and showed " insufficient virtual memory"
thanks so much for your time!

Code:

MemTotal:       132135956 kB






Code:
processor   : 63
vendor_id   : GenuineIntel
cpu family   : 6
model      : 45
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
stepping   : 7
cpu MHz      : 1200.000
cache size   : 20480 KB
physical id   : 3
siblings   : 16
core id      : 7
cpu cores   : 8
apicid      : 111
initial apicid   : 111
fpu      : yes
fpu_exception   : yes
cpuid level   : 13
wp      : yes
flags      : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid
bogomips   : 4799.38
clflush size   : 64
cache_alignment   : 64
address sizes   : 46 bits physical, 48 bits virtual









Code:





model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
model name   : Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
physical id   : 0
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