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Old   February 11, 2009, 07:38
Default Dear all, I tried to run LES
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Ivan Lau
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Dear all,
I tried to run LES with timeVaryingMappedPatch
However, I got the following error

Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'

--------------------------------------------
I found some information from the website:
Step 1: Find out the current limit

To find out the current file descripter limit for a given use, log in as the particular user and run the following command.

$ ulimit -n

By default on Debian it would be 1024.

Step 2: Increase the limit

You would have to edit /etc/security/limits.conf. You will find details on how to setup different limits in limits.conf itself. The record that you have to put in should look like the following.

username hard nofile 2048

Step 3: Log out and Log back in

You would have to log out and log back in as the user that we updated the file descripter limit. Then run the following command.

$ ulimit -n

You should see the updated file descripter limit.

------------------------------------------------
However, the solution above is for general Linux case. Now, it is related to OpenFOAM. Does anyone what happen to this? Can I continue?

Regards,
Ivan
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Old   February 11, 2009, 09:56
Default Hi Ivan! Are you
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Bernhard Gschaider
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Hi Ivan!

<bernhard> Are you using by any chance PyFoam to run your solver? Because the error and the message looks suspiciously like something PyFoam would say when it has to open a huge lot of files in the analyzed directory. Usually because it can't tell one timestep from the next and therefor opens a new file for (for instance) for every solver call. So it might be a PyFoam problem. If so: could you tell me which solver it is (some have a different format for "Time = 3.45" and then PyFoam can't distinguish time-steps) and could you check whether for consecutive time-steps the "Time = " LEXICALLY differs (for instance with "Time = 1.000456" and a time-step of 10^-7 the next timestep might print "Time = 1.000456" too)

Bernhard
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Old   February 11, 2009, 12:17
Default Hi, Bernhard, You are so ri
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Ivan Lau
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Hi, Bernhard,

You are so right! I use your pyFoamPlotRunner.py script to run LES (solver = oodles).

My time step = 0.0005s and write interval = 0.005s
This error start to around 1.2s (I resume the run from 0.5s).

The consecutive time step should be ok as I allow enough significant number.

Anyway, I hope this is helpful. Thanks for your quick reply. Please advise what I should do as I plan to stop the solver and run from the previous steps.

Should I restart from the "first" time step that has this error? Or, can I let it continue from last time step?

Regards,
Ivan

-- A sample log is as the follow: --
Time = 1.2735

Courant Number mean: 0.00055676365 max: 0.65250404
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
Saving old-time boundary values of U::outlet
Boundary gradient of U::outlet has already been updated
Boundary gradient of U::outlet has already been updated
DILUPBiCG: Solving for Ux, Initial residual = 0.00022111803, Final residual = 3.7128709e-09, No Iterations 1
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
DILUPBiCG: Solving for Uy, Initial residual = 0.003009986, Final residual = 6.0641951e-08, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.0021211077, Final residual = 3.167597e-08, No Iterations 1
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
GAMG: Solving for p, Initial residual = 0.067676383, Final residual = 9.03386e-07, No Iterations 94
GAMG: Solving for p, Initial residual = 8.6775994e-07, Final residual = 8.6775994e-07, No Iterations 0
GAMG: Solving for p, Initial residual = 8.6775994e-07, Final residual = 8.6775994e-07, No Iterations 0
time step continuity errors : sum local = 1.1017799e-12, global = 1.3554078e-13, cumulative = -5.9256848e-12
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
GAMG: Solving for p, Initial residual = 9.1227694e-05, Final residual = 9.7391603e-07, No Iterations 9
GAMG: Solving for p, Initial residual = 9.7391419e-07, Final residual = 9.7391419e-07, No Iterations 0
GAMG: Solving for p, Initial residual = 9.7391419e-07, Final residual = 9.7391419e-07, No Iterations 0
time step continuity errors : sum local = 1.2365641e-12, global = -2.2237115e-13, cumulative = -6.148056e-12
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
ExecutionTime = 103027.35 s ClockTime = 105399 s

Calculating averages

Time = 1.274

Courant Number mean: 0.00055674882 max: 0.65367521
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
Saving old-time boundary values of U::outlet
Boundary gradient of U::outlet has already been updated
Boundary gradient of U::outlet has already been updated
DILUPBiCG: Solving for Ux, Initial residual = 0.00023278593, Final residual = 3.8494851e-09, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0030740255, Final residual = 6.0290512e-08, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.002194585, Final residual = 3.2188904e-08, No Iterations 1
GAMG: Solving for p, Initial residual = 0.058895772, Final residual = 8.8040836e-07, No Iterations 86
GAMG: Solving for p, Initial residual = 8.6251892e-07, Final residual = 8.6251892e-07, No Iterations 0
GAMG: Solving for p, Initial residual = 8.6251892e-07, Final residual = 8.6251892e-07, No Iterations 0
time step continuity errors : sum local = 1.1464957e-12, global = -1.298191e-13, cumulative = -6.2778751e-12
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
GAMG: Solving for p, Initial residual = 8.5971209e-05, Final residual = 8.7121062e-07, No Iterations 10
GAMG: Solving for p, Initial residual = 8.7121287e-07, Final residual = 8.7121287e-07, No Iterations 0
GAMG: Solving for p, Initial residual = 8.7121287e-07, Final residual = 8.7121287e-07, No Iterations 0
time step continuity errors : sum local = 1.1580491e-12, global = -2.3653425e-13, cumulative = -6.5144093e-12
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
ExecutionTime = 103084.46 s ClockTime = 105456 s

Calculating averages

Time = 1.2745

Courant Number mean: 0.00055674721 max: 0.65478406
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
Saving old-time boundary values of U::outlet
Boundary gradient of U::outlet has already been updated
Boundary gradient of U::outlet has already been updated
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
DILUPBiCG: Solving for Ux, Initial residual = 0.0002272263, Final residual = 3.7851613e-09, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0030371887, Final residual = 5.9868971e-08, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.002188867, Final residual = 3.1912482e-08, No Iterations 1
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/28165/status'
GAMG: Solving for p, Initial residual = 0.053964779, Final residual = 9.4404547e-07, No Iterations 76
GAMG: Solving for p, Initial residual = 9.215077e-07, Final residual = 9.215077e-07, No Iterations 0
GAMG: Solving for p, Initial residual = 9.215077e-07, Final residual = 9.215077e-07, No Iterations 0
time step continuity errors : sum local = 1.2835445e-12, global = 1.4119057e-13, cumulative = -6.3732188e-12
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
GAMG: Solving for p, Initial residual = 8.0300075e-05, Final residual = 8.6677323e-07, No Iterations 10
GAMG: Solving for p, Initial residual = 8.6677062e-07, Final residual = 8.6677062e-07, No Iterations 0
GAMG: Solving for p, Initial residual = 8.6677062e-07, Final residual = 8.6677062e-07, No Iterations 0
time step continuity errors : sum local = 1.2073061e-12, global = 2.3840291e-13, cumulative = -6.1348159e-12
Updating boundary gradient of U::outlet by CrankNicholson and normal schemes
ExecutionTime = 103137.21 s ClockTime = 105509 s
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Old   February 11, 2009, 13:57
Default Hi Ivan! Restart shouldn't
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Bernhard Gschaider
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Hi Ivan!

Restart shouldn't be a problem.

Could you check the PyFoamRunner.oodles.analyzed-directory (name may be slightly different depending on the PyFoam-Version) how many files are there (my suspcion is it should be hundreds for that error to occur).

Which options are you using for the Runner? Are you using a customRegexp-file? Does the same error occur when you do "pyFoamPlotWatcher.py PyFoamRunner.oodles.logfile" (again: fileame may be slightly different)

Strange.

Bernhard
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Old   February 19, 2009, 03:43
Default Hi Bernhard, Sorry, I didn'
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Ivan Lau
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Hi Bernhard,

Sorry, I didn't notice your reply and I was working on something else during this period.
I restarted it too without using pyFoamPlotRunner.py!

ulimit -n gives me 1024 which is default.
Yes, it is over 1024, and this is the error.

I didn't set any option, I just do
pyFoamPlotRunner.py (not pyFoamPlotWatcher.py) mpirun --hostfile ... oodles -parallel

Oops! As my harddrive was full, I cleaned up and lost that folder. Sorry.

Regards,
ivan
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Old   July 1, 2009, 04:31
Default
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Jean-Peer Lorenz
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Hi Bernhard,

I just stumbled over the problems mentioned above. The PyFoamRunner crashed with error "IOError: [Errno 24] Too many open files". Here are the last log lines.

Code:
Time = 1.99539

MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.29231e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.29182e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.29134e-20  Max(gamma) = 1.00028
DICPCG:  Solving for pd, Initial residual = 0.0113928, Final residual = 0.00010687, No Iterations 19
DICPCG:  Solving for pd, Initial residual = 0.00249276, Final residual = 2.2737e-05, No Iterations 36
DICPCG:  Solving for pd, Initial residual = 0.003959, Final residual = 3.87538e-05, No Iterations 23
DICPCG:  Solving for pd, Initial residual = 0.00119743, Final residual = 9.91234e-08, No Iterations 101
time step continuity errors : sum local = 1.82447e-15, global = -1.24033e-16, cumulative = 3.29632e-06
ExecutionTime = 61591 s  ClockTime = 61681 s

Courant Number mean: 1.54139e-06 max: 0.284435
deltaT = 1.58918e-07
forces output:
forces(pressure, viscous)((-32447.5 308193 103836) (8.14909 -2.4303 21.7292))
moment(pressure, viscous)((21540.8 -126202 407786) (-1.72709 -28.5359 -1.59926))

Time = 1.99539

MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.29083e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.29032e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28981e-20  Max(gamma) = 1.00028
DICPCG:  Solving for pd, Initial residual = 0.0108749, Final residual = 0.000104919, No Iterations 29
DICPCG:  Solving for pd, Initial residual = 0.0029968, Final residual = 2.83445e-05, No Iterations 28
DICPCG:  Solving for pd, Initial residual = 0.00395811, Final residual = 3.72463e-05, No Iterations 25
DICPCG:  Solving for pd, Initial residual = 0.00122734, Final residual = 9.73827e-08, No Iterations 102
time step continuity errors : sum local = 1.9901e-15, global = -1.28899e-16, cumulative = 3.29632e-06
ExecutionTime = 61601.5 s  ClockTime = 61691 s

Courant Number mean: 1.62088e-06 max: 0.283189
deltaT = 1.68352e-07
forces output:
forces(pressure, viscous)((-33706.2 320823 107013) (8.01442 -2.15802 21.6129))
moment(pressure, viscous)((21981.8 -129859 422299) (-1.72472 -28.3819 -1.2422))

Time = 1.99539

MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28927e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28873e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28818e-20  Max(gamma) = 1.00028
DICPCG:  Solving for pd, Initial residual = 0.0109102, Final residual = 9.56347e-05, No Iterations 18
DICPCG:  Solving for pd, Initial residual = 0.00239302, Final residual = 2.372e-05, No Iterations 35
DICPCG:  Solving for pd, Initial residual = 0.00372946, Final residual = 3.34371e-05, No Iterations 25
DICPCG:  Solving for pd, Initial residual = 0.00118738, Final residual = 9.95898e-08, No Iterations 100
time step continuity errors : sum local = 2.27052e-15, global = -3.92834e-17, cumulative = 3.29632e-06
ExecutionTime = 61611.7 s  ClockTime = 61701 s

Courant Number mean: 1.71202e-06 max: 0.286551
deltaT = 1.7625e-07
forces output:
forces(pressure, viscous)((-34023.9 324833 109190) (7.86349 -1.81874 21.5097))
moment(pressure, viscous)((22450.6 -132479 427404) (-1.72513 -28.2456 -0.797366))

Time = 1.99539

MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28761e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28704e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28647e-20  Max(gamma) = 1.00028
DICPCG:  Solving for pd, Initial residual = 0.0117827, Final residual = 0.000109719, No Iterations 31
DICPCG:  Solving for pd, Initial residual = 0.00365853, Final residual = 3.65785e-05, No Iterations 32
DICPCG:  Solving for pd, Initial residual = 0.00400006, Final residual = 3.46489e-05, No Iterations 28
DICPCG:  Solving for pd, Initial residual = 0.00122108, Final residual = 9.59937e-08, No Iterations 110
time step continuity errors : sum local = 2.37101e-15, global = -9.83986e-17, cumulative = 3.29632e-06
ExecutionTime = 61622.7 s  ClockTime = 61712 s

Courant Number mean: 1.78704e-06 max: 0.297048
deltaT = 1.78001e-07
forces output:
forces(pressure, viscous)((-34438.1 329168 109112) (7.70367 -1.43348 21.4606))
moment(pressure, viscous)((22279.2 -132147 431162) (-1.73255 -28.18 -0.29189))

Time = 1.99539

MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28589e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28531e-20  Max(gamma) = 1.00028
MULES: Solving for gamma
Liquid phase volume fraction = 0.923305  Min(gamma) = -6.28473e-20  Max(gamma) = 1.00028
DICPCG:  Solving for pd, Initial residual = 0.00987204, Final residual = 8.25315e-05, No Iterations 20
DICPCG:  Solving for pd, Initial residual = 0.00218102, Final residual = 1.97917e-05, No Iterations 36
DICPCG:  Solving for pd, Initial residual = 0.00349928, Final residual = 3.23379e-05, No Iterations 25
DICPCG:  Solving for pd, Initial residual = 0.00112364, Final residual = 9.77603e-08, No Iterations 101
time step continuity errors : sum local = 2.39084e-15, global = -1.01181e-16, cumulative = 3.29632e-06
ExecutionTime = 61633.1 s  ClockTime = 61723 s
Traceback (most recent call last):
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/bin/pyFoamRunner.py", line 5, in ?
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Applications/Runner.py", line 52, in __init__
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Applications/PyFoamApplication.py", line 103, in __init_
_
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Applications/Runner.py", line 104, in run
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Execution/BasicRunner.py", line 196, in start
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Execution/AnalyzedRunner.py", line 20, in lineHandle
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Execution/AnalyzedCommon.py", line 45, in lineHandle
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 80, in analyzeLine
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/LogAnalysis/GeneralLineAnalyzer.py", line 71, in doAnaly
sis
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/LogAnalysis/ExecutionTimeLineAnalyzer.py", line 68, in a
ddToFiles
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Basics/OutFileCollection.py", line 83, in write
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Basics/OutputFile.py", line 45, in write
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Basics/BasicFile.py", line 48, in writeLine
  File "/home/acuser3/OpenFOAM/ThirdParty/Python/lib/python2.3/site-packages/PyFoam/Basics/BasicFile.py", line 38, in getHandle
IOError: [Errno 24] Too many open files: './wig_06_u.rasInterFoam.analyzed/wallClockTime_113'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/15241/status'
Getting LinuxMem: [Errno 24] Too many open files: '/proc/15241/status'
The solver I am using is rasInterFoam. The PyFoamRunner was invoked using the command "nohup pyFoamRunner.py --clear-case --procnr=16 --machinefile=hosts --logname=logfile rasInterFoam >& log.out &". The timestep is quite small, so I suppose that is the problem as you stated.

If you need additional information just tell.

Regards,
Jean-Peer
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Old   July 1, 2009, 10:16
Default
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Bernhard Gschaider
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Quote:
Originally Posted by jploz View Post
Hi Bernhard,

I just stumbled over the problems mentioned above. The PyFoamRunner crashed with error "IOError: [Errno 24] Too many open files". Here are the last log lines.

Code:
Time = 1.99539

<snip>

Courant Number mean: 1.54139e-06 max: 0.284435
deltaT = 1.58918e-07

<snip>

Time = 1.99539

<snip>
The solver I am using is rasInterFoam. The PyFoamRunner was invoked using the command "nohup pyFoamRunner.py --clear-case --procnr=16 --machinefile=hosts --logname=logfile rasInterFoam >& log.out &". The timestep is quite small, so I suppose that is the problem as you stated.

If you need additional information just tell.
No. The problem is definitely that PyFoam can't distinguish the time-steps. And I'm not quite sure whether I want to change this behaviour

Try this to fix this: set timePrecision in system/controlDict to a higher value (9 should be sufficient for your case). This should (never tried it) give you more digits of the time and thus the chance to distinguish the time-steps

Bernhard
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