Installing dedalus on CentOS 6.5 platform

[Ghanesh Narasimhan]

Dear All,

I am Ghanesh , Masters student from Centre for Earth Sciences, Indian Institute of Science, Bangalore. I am a new user trying to install dedalus on my workstation running CentOS 6.5 platform, but I am facing some difficulty.
I used the install.sh script , but ended with errors as there was no activate file to be run in the final step. I have attached the dedalus_install.log file containing the output that I got by running the attached the install.sh file .

Also, pip install matplotlib killed the install process right away and hence, I commented the lines 632-634 to avoid installing matplotlib via install.sh and installed it seperately . But I was running into an error saying activate file not found . I also, checked that activate file is not there in the repository. I don't know if install.sh can be used or not. So, its not clear to me on how should I install on Cent OS platform .
   
Hence, please, help me out, how should I install dedalus on Cent OS platform ?

Regards,
Ghanesh

[j s oishi]

Hi Ghanesh,

Thanks for your interest in Dedalus! Sorry to hear the install was not so smooth for you. We're still working out the bugs in the install script, and you are the first person to try it on CentOS. I'm pretty sure with a little bit of help from you, we should be able to get it working.

First of all, there was a bug in the install script which I have now fixed that kept the activate script from appearing in the repository, just as you said. Thanks for alerting us to it! I've fixed it, and you can download the updated install script here:

https://bitbucket.org/dedalus-project/dedalus2/raw/a2b5fe3b8858384ac8e730c79b2677369af17aa4/docs/install.sh

You can download that and copy it over your current install script. Do

$ rm -rf path/to/dedalus/src/dedalus2

and then

$ bash install.sh

and it will simply reinstall dedalus itself, and not all the prerequisites.

I need to know a bit more about the matplotlib failure. Could you tell me what it says on the command line when it fails?

Finally, as you saw during install, we don't have the complete list of prerequisite packages for RedHat (which is the upstream distribution for CentOS). You'll need to have installed a bunch of packages, including mpi, atlas, mercurial, and others. It sounds like you probably have all these packages already. If you could help us by telling us what they're all called in CentOS, that would be helpful.

thanks,

Jeff

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[Ghanesh Narasimhan]

Hi Jeff,

Thanks for the help. I am yet to try your solutions and try reinstalling . Will do it shortly.

But, I also have few more doubts about the code. I am completely new to this code and also, I have just started learning spectral methods.
 
So my questons might be very basic, so please forgive me in such a case, and then, here goes my doubts :

a) How is the pressure treated in the code for an incompressible problem ? Does the code solve for pressure by the conventional pressure poisson equation ?

b) Can the code solve equations with anelastic/boussinesq incompressible approximations ? How are the div(u)=0 and div(b)=0 divergence free conditions ensured in the code? 

c) Considering a 2d problem in a bounded domain, Is it possible to apply different boundary conditions for velocity and current ? 
  i.e Can we give for velocity -  no-slip BC,stress-free BC,  symmetric and asymmetric BCs , and similarly  can we give  for current - conducting / insulating BC ?

d) Can the problems be solved in cylindrical and spherical polar coordinates also  ?

e) How does the code scale when run parallelly ?
 
Thanks and regards,
Ghanesh

[Daniel Lecoanet]

Hi Ghanesh,

See answers to your questions below.

On Sat, Nov 1, 2014 at 10:29 AM, Ghanesh Narasimhan <ghan...@gmail.com> wrote:

Hi Jeff,

Thanks for the help. I am yet to try your solutions and try reinstalling . Will do it shortly.

But, I also have few more doubts about the code. I am completely new to this code and also, I have just started learning spectral methods.
 
So my questons might be very basic, so please forgive me in such a case, and then, here goes my doubts :

a) How is the pressure treated in the code for an incompressible problem ? Does the code solve for pressure by the conventional pressure poisson equation ?

If you want, you can write a poisson equation for the pressure for incompressible flow.  However, Dedalus does not require an equation that explicitly gives the pressure in order to solve for the pressure.  For instance, if you just use just use the momentum equation and div(u)=0, then the div(u)=0 equation becomes the equation for pressure.  This is done on the front page of our documentation:

http://dedalus-project.readthedocs.org/en/latest/

 

b) Can the code solve equations with anelastic/boussinesq incompressible approximations ? How are the div(u)=0 and div(b)=0 divergence free conditions ensured in the code? 

Yes.  As before, you just implement div(u)=0 and div(b)=0 as equations.

 

c) Considering a 2d problem in a bounded domain, Is it possible to apply different boundary conditions for velocity and current ? 
  i.e Can we give for velocity -  no-slip BC,stress-free BC,  symmetric and asymmetric BCs , and similarly  can we give  for current - conducting / insulating BC ?

Yes, BCs are just implemented as strings.  See e.g., dedalus2/examples/2d_ivp/rayleigh_benard for an example of this.

 

d) Can the problems be solved in cylindrical and spherical polar coordinates also  ?

Right now, problems can be solved for cylindrical shells, as long as you're ok with being periodic in z.  We are working on spherical geometry.

 

e) How does the code scale when run parallelly ?
 

We've run Dedalus on up to 4096 processors without much loss of efficiency.

 

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/1ee0af2f-8bea-41ad-9b31-c905b4330203%40googlegroups.com.

[Ghanesh Narasimhan]

Thanks for the reply Daniel.

I think I have partially installed the dedalus code on CentOS ,as:

a) the matplotlib is not working properly. The pip installing is not working . So I manually did yum install python-matplotlib and matplotlib was installed. But when I ran exmaples of 1d_ivp and 2d_ivp, it says matplotlib is not found. So, I think I should specify export the path of installed matplotlib, but then  how should I specify the path for matplotlib ?

b) The 2d-rayleigh benard problem ran smoothly when the code was run serially. I also got the snapshot files during the serial run.
   
But when I ran parallelly with 4 processors,  it initially gave segmentation fault which I overcame by typing the command "ulimit -s unlimited" and then I again ran the code and at the 121th iteration and got the following errors printed where it says some files could not be opened. Would it be due to improper installation of matplotlib or is it due to any other reason  ? .  This happens when I run the code with more than 1 processor.

Thanks and regards,

Ghanesh

 
1) SEGMENTATION FAULT ERROR:
 $bash : /home/ghanesh/mpich-install/bin/mpiexec -np 4 python3 rayleigh_benard.py

2014-11-02 14:19:48,990 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 8s, Rate: 2.2e+01/s
2014-11-02 14:19:49,001 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 8s, Rate: 2.2e+01/s
2014-11-02 14:19:49,002 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 8s, Rate: 2.1e+01/s
2014-11-02 14:19:49,005 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 7s, Rate: 2.3e+01/s
2014-11-02 14:19:49,328 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.8e+01/s
2014-11-02 14:19:49,329 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.7e+01/s
2014-11-02 14:19:49,330 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.9e+01/s
2014-11-02 14:19:49,335 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.7e+01/s
2014-11-02 14:19:49,675 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 5.0e+01/s
2014-11-02 14:19:49,676 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 5.0e+01/s
2014-11-02 14:19:49,688 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 4.9e+01/s
2014-11-02 14:19:49,688 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 4.8e+01/s
2014-11-02 14:19:50,020 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 5.1e+01/s
2014-11-02 14:19:50,023 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 5.1e+01/s
2014-11-02 14:19:50,041 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 5.0e+01/s
2014-11-02 14:19:50,050 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 4.9e+01/s
2014-11-02 14:19:50,388 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 1s, Remaining: 2s, Rate: 5.0e+01/s
2014-11-02 14:19:50,414 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 1s, Remaining: 2s, Rate: 4.9e+01/s
2014-11-02 14:19:50,465 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 2s, Remaining: 2s, Rate: 4.8e+01/s
2014-11-02 14:19:50,467 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 2s, Remaining: 2s, Rate: 4.8e+01/s
2014-11-02 14:19:50,745 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 5.0e+01/s
2014-11-02 14:19:50,800 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 4.9e+01/s
2014-11-02 14:19:50,811 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 4.9e+01/s
2014-11-02 14:19:50,815 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 4.8e+01/s
2014-11-02 14:19:51,102 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 5.0e+01/s
2014-11-02 14:19:51,158 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:19:51,161 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:19:51,173 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:19:51,459 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 3s, Remaining: 1s, Rate: 5.0e+01/s
2014-11-02 14:19:51,504 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 3s, Remaining: 1s, Rate: 5.0e+01/s
2014-11-02 14:19:51,523 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 3s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:19:51,540 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 3s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:19:51,817 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 5.0e+01/s
2014-11-02 14:19:51,851 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 5.0e+01/s
2014-11-02 14:19:51,872 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:19:51,926 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 4.8e+01/s
2014-11-02 14:19:52,175 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:19:52,197 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:19:52,222 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:19:52,307 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 4.8e+01/s
2014-11-02 14:19:52,355 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:19:52,360 __main__ 0/1 INFO :: Solver built
2014-11-02 14:19:52,370 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:19:52,371 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:19:52,376 __main__ 0/1 INFO :: Solver built
2014-11-02 14:19:52,386 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:19:52,398 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:19:52,403 __main__ 0/1 INFO :: Solver built
2014-11-02 14:19:52,413 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:19:52,522 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 4s, Remaining: 0s, Rate: 4.8e+01/s
2014-11-02 14:19:52,528 __main__ 0/1 INFO :: Solver built
2014-11-02 14:19:52,538 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:19:52,569 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:19:52,582 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:19:52,607 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:19:52,756 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:19:54,079 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:19:54,079 __main__ 0/1 INFO :: Run time: 1.693633
2014-11-02 14:19:54,079 __main__ 0/1 INFO :: Iterations: 10
Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 488, in process
    dset.id.write(memory_space, file_space, out.data)
  File "h5d.pyx", line 219, in h5py.h5d.DatasetID.write (h5py/h5d.c:3069)
  File "_proxy.pyx", line 132, in h5py._proxy.dset_rw (h5py/_proxy.c:1721)
  File "_proxy.pyx", line 93, in h5py._proxy.H5PY_H5Dwrite (h5py/_proxy.c:1456)
OSError: Can't prepare for writing data (Addr overflow, addr = 2292440, size=16896, eoa=2241752)
Exception ignored in: 'h5py._objects.ObjectID.__dealloc__'
Traceback (most recent call last):
  File "_objects.pyx", line 250, in h5py._objects.ObjectID.__dealloc__ (h5py/_objects.c:3295)
  File "_objects.pyx", line 212, in h5py._objects._Registry.__delitem__ (h5py/_objects.c:2670)
OSError: Driver write request failed (Addr overflow, addr = 2241752, size = 16896, eoa = 2241752)
[localhost:32381] *** Process received signal ***
[localhost:32381] Signal: Segmentation fault (11)
[localhost:32381] Signal code: Address not mapped (1)
[localhost:32381] Failing at address: (nil)
[localhost:32381] [ 0] /lib64/libpthread.so.0[0x3ce240f710]
[localhost:32381] [ 1] /usr/lib64/libhdf5.so.8(H5D_close+0x21)[0x7fe8503da621]
[localhost:32381] [ 2] /usr/lib64/libhdf5.so.8(H5I_clear_type+0x9c)[0x7fe8504695fc]
[localhost:32381] [ 3] /usr/lib64/libhdf5.so.8(H5D_term_interface+0x39)[0x7fe8503dd419]
[localhost:32381] [ 4] /usr/lib64/libhdf5.so.8(H5_term_library+0xd5)[0x7fe850389ad5]
[localhost:32381] [ 5] /lib64/libc.so.6(exit+0xe2)[0x3ce2035e22]
[localhost:32381] [ 6] /lib64/libc.so.6(__libc_start_main+0x104)[0x3ce201ed24]
[localhost:32381] [ 7] python3[0x41a1e9]
[localhost:32381] *** End of error message ***
2014-11-02 14:19:54,219 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:19:54,250 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:19:54,423 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:19:55,387 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:19:55,387 __main__ 0/1 INFO :: Run time: 2.974692
2014-11-02 14:19:55,388 __main__ 0/1 INFO :: Iterations: 18
Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 488, in process
    dset.id.write(memory_space, file_space, out.data)
  File "h5d.pyx", line 219, in h5py.h5d.DatasetID.write (h5py/h5d.c:3069)
  File "_proxy.pyx", line 132, in h5py._proxy.dset_rw (h5py/_proxy.c:1721)
  File "_proxy.pyx", line 93, in h5py._proxy.H5PY_H5Dwrite (h5py/_proxy.c:1456)
OSError: Can't prepare for writing data (Addr overflow, addr = 6062168, size=3136, eoa=6045272)
2014-11-02 14:19:55,563 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:19:55,563 __main__ 0/1 INFO :: Run time: 3.024741
2014-11-02 14:19:55,563 __main__ 0/1 INFO :: Iterations: 18
Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 488, in process
    dset.id.write(memory_space, file_space, out.data)
  File "h5d.pyx", line 219, in h5py.h5d.DatasetID.write (h5py/h5d.c:3069)
  File "_proxy.pyx", line 132, in h5py._proxy.dset_rw (h5py/_proxy.c:1721)
  File "_proxy.pyx", line 93, in h5py._proxy.H5PY_H5Dwrite (h5py/_proxy.c:1456)
OSError: Can't prepare for writing data (Addr overflow, addr = 6062168, size=3136, eoa=6045272)
2014-11-02 14:19:55,825 __main__ 0/1 INFO :: Iteration: 21, Time: 2.410000e-01, dt: 1.331000e-02
2014-11-02 14:19:56,603 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:19:56,603 __main__ 0/1 INFO :: Run time: 4.232718
2014-11-02 14:19:56,603 __main__ 0/1 INFO :: Iterations: 26
Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 488, in process
    dset.id.write(memory_space, file_space, out.data)
  File "h5d.pyx", line 219, in h5py.h5d.DatasetID.write (h5py/h5d.c:3069)
  File "_proxy.pyx", line 132, in h5py._proxy.dset_rw (h5py/_proxy.c:1721)
  File "_proxy.pyx", line 93, in h5py._proxy.H5PY_H5Dwrite (h5py/_proxy.c:1456)
OSError: Can't prepare for writing data (Wrong b-tree signature)

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 32379 RUNNING AT localhost.localdomain
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

TYPING ulimit -s unlimited AND RERUNNING THE CODE:
(dedalus)[ghanesh@localhost rayleigh_benard]$ ulimit -s unlimited

(dedalus)[ghanesh@localhost rayleigh_benard]$ /home/ghanesh/mpich-install/bin/mpiexec -np 4 python3 rayleigh_benard.py

2014-11-02 14:20:39,243 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 8s, Rate: 2.3e+01/s
2014-11-02 14:20:39,245 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 8s, Rate: 2.3e+01/s
2014-11-02 14:20:39,245 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 7s, Rate: 2.3e+01/s
2014-11-02 14:20:39,250 solvers 0/1 INFO :: Building pencil matrix 1/171 (~1%) Elapsed: 0s, Remaining: 8s, Rate: 2.2e+01/s
2014-11-02 14:20:39,569 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.9e+01/s
2014-11-02 14:20:39,572 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.9e+01/s
2014-11-02 14:20:39,574 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.8e+01/s
2014-11-02 14:20:39,594 solvers 0/1 INFO :: Building pencil matrix 18/171 (~11%) Elapsed: 0s, Remaining: 3s, Rate: 4.6e+01/s
2014-11-02 14:20:39,917 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 5.0e+01/s
2014-11-02 14:20:39,926 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 5.0e+01/s
2014-11-02 14:20:39,966 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 4.7e+01/s
2014-11-02 14:20:40,071 solvers 0/1 INFO :: Building pencil matrix 36/171 (~21%) Elapsed: 1s, Remaining: 3s, Rate: 4.1e+01/s
2014-11-02 14:20:40,264 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 5.1e+01/s
2014-11-02 14:20:40,278 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 5.0e+01/s
2014-11-02 14:20:40,333 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 2s, Rate: 4.8e+01/s
2014-11-02 14:20:40,447 solvers 0/1 INFO :: Building pencil matrix 54/171 (~32%) Elapsed: 1s, Remaining: 3s, Rate: 4.3e+01/s
2014-11-02 14:20:40,609 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 1s, Remaining: 2s, Rate: 5.1e+01/s
2014-11-02 14:20:40,630 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 1s, Remaining: 2s, Rate: 5.0e+01/s
2014-11-02 14:20:40,687 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 1s, Remaining: 2s, Rate: 4.9e+01/s
2014-11-02 14:20:40,822 solvers 0/1 INFO :: Building pencil matrix 72/171 (~42%) Elapsed: 2s, Remaining: 2s, Rate: 4.4e+01/s
2014-11-02 14:20:40,956 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 5.1e+01/s
2014-11-02 14:20:40,983 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 5.0e+01/s
2014-11-02 14:20:41,043 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 4.9e+01/s
2014-11-02 14:20:41,207 solvers 0/1 INFO :: Building pencil matrix 90/171 (~53%) Elapsed: 2s, Remaining: 2s, Rate: 4.5e+01/s
2014-11-02 14:20:41,309 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 5.1e+01/s
2014-11-02 14:20:41,336 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 5.1e+01/s
2014-11-02 14:20:41,397 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:20:41,597 solvers 0/1 INFO :: Building pencil matrix 108/171 (~63%) Elapsed: 2s, Remaining: 1s, Rate: 4.5e+01/s
2014-11-02 14:20:41,656 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 2s, Remaining: 1s, Rate: 5.1e+01/s
2014-11-02 14:20:41,690 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 2s, Remaining: 1s, Rate: 5.1e+01/s
2014-11-02 14:20:41,753 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 3s, Remaining: 1s, Rate: 4.9e+01/s
2014-11-02 14:20:41,985 solvers 0/1 INFO :: Building pencil matrix 126/171 (~74%) Elapsed: 3s, Remaining: 1s, Rate: 4.5e+01/s
2014-11-02 14:20:42,003 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 5.1e+01/s
2014-11-02 14:20:42,044 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 5.1e+01/s
2014-11-02 14:20:42,107 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 5.0e+01/s
2014-11-02 14:20:42,351 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 5.1e+01/s
2014-11-02 14:20:42,365 solvers 0/1 INFO :: Building pencil matrix 144/171 (~84%) Elapsed: 3s, Remaining: 1s, Rate: 4.6e+01/s
2014-11-02 14:20:42,397 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 5.1e+01/s
2014-11-02 14:20:42,462 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:20:42,525 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 3s, Remaining: 0s, Rate: 5.1e+01/s
2014-11-02 14:20:42,531 __main__ 0/1 INFO :: Solver built
2014-11-02 14:20:42,540 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:20:42,576 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 3s, Remaining: 0s, Rate: 5.1e+01/s
2014-11-02 14:20:42,581 __main__ 0/1 INFO :: Solver built
2014-11-02 14:20:42,591 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:20:42,642 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 3s, Remaining: 0s, Rate: 5.0e+01/s
2014-11-02 14:20:42,648 __main__ 0/1 INFO :: Solver built
2014-11-02 14:20:42,657 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:20:42,739 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:20:42,763 solvers 0/1 INFO :: Building pencil matrix 162/171 (~95%) Elapsed: 4s, Remaining: 0s, Rate: 4.5e+01/s
2014-11-02 14:20:42,805 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:20:42,849 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:20:42,946 solvers 0/1 INFO :: Building pencil matrix 171/171 (~100%) Elapsed: 4s, Remaining: 0s, Rate: 4.6e+01/s
2014-11-02 14:20:42,952 __main__ 0/1 INFO :: Solver built
2014-11-02 14:20:42,961 __main__ 0/1 INFO :: Starting loop
2014-11-02 14:20:43,159 __main__ 0/1 INFO :: Iteration: 1, Time: 1.000000e-02, dt: 1.100000e-02
2014-11-02 14:20:44,361 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:20:44,452 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:20:44,480 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:20:44,836 __main__ 0/1 INFO :: Iteration: 11, Time: 1.200000e-01, dt: 1.210000e-02
2014-11-02 14:20:45,988 __main__ 0/1 INFO :: Iteration: 21, Time: 2.410000e-01, dt: 1.331000e-02
2014-11-02 14:20:46,076 __main__ 0/1 INFO :: Iteration: 21, Time: 2.410000e-01, dt: 1.331000e-02
2014-11-02 14:20:46,105 __main__ 0/1 INFO :: Iteration: 21, Time: 2.410000e-01, dt: 1.331000e-02
2014-11-02 14:20:46,523 __main__ 0/1 INFO :: Iteration: 21, Time: 2.410000e-01, dt: 1.331000e-02
2014-11-02 14:20:47,597 __main__ 0/1 INFO :: Iteration: 31, Time: 3.741000e-01, dt: 1.464100e-02
2014-11-02 14:20:47,696 __main__ 0/1 INFO :: Iteration: 31, Time: 3.741000e-01, dt: 1.464100e-02
2014-11-02 14:20:47,721 __main__ 0/1 INFO :: Iteration: 31, Time: 3.741000e-01, dt: 1.464100e-02
2014-11-02 14:20:48,167 __main__ 0/1 INFO :: Iteration: 31, Time: 3.741000e-01, dt: 1.464100e-02
2014-11-02 14:20:49,227 __main__ 0/1 INFO :: Iteration: 41, Time: 5.205100e-01, dt: 1.610510e-02
2014-11-02 14:20:49,359 __main__ 0/1 INFO :: Iteration: 41, Time: 5.205100e-01, dt: 1.610510e-02
2014-11-02 14:20:49,363 __main__ 0/1 INFO :: Iteration: 41, Time: 5.205100e-01, dt: 1.610510e-02
2014-11-02 14:20:49,826 __main__ 0/1 INFO :: Iteration: 41, Time: 5.205100e-01, dt: 1.610510e-02
2014-11-02 14:20:50,860 __main__ 0/1 INFO :: Iteration: 51, Time: 6.815610e-01, dt: 1.771561e-02
2014-11-02 14:20:50,996 __main__ 0/1 INFO :: Iteration: 51, Time: 6.815610e-01, dt: 1.771561e-02
2014-11-02 14:20:51,020 __main__ 0/1 INFO :: Iteration: 51, Time: 6.815610e-01, dt: 1.771561e-02
2014-11-02 14:20:51,485 __main__ 0/1 INFO :: Iteration: 51, Time: 6.815610e-01, dt: 1.771561e-02
2014-11-02 14:20:52,513 __main__ 0/1 INFO :: Iteration: 61, Time: 8.587171e-01, dt: 1.948717e-02
2014-11-02 14:20:52,646 __main__ 0/1 INFO :: Iteration: 61, Time: 8.587171e-01, dt: 1.948717e-02
2014-11-02 14:20:52,695 __main__ 0/1 INFO :: Iteration: 61, Time: 8.587171e-01, dt: 1.948717e-02
2014-11-02 14:20:53,158 __main__ 0/1 INFO :: Iteration: 61, Time: 8.587171e-01, dt: 1.948717e-02
2014-11-02 14:20:54,168 __main__ 0/1 INFO :: Iteration: 71, Time: 1.053589e+00, dt: 2.143589e-02
2014-11-02 14:20:54,297 __main__ 0/1 INFO :: Iteration: 71, Time: 1.053589e+00, dt: 2.143589e-02
2014-11-02 14:20:54,353 __main__ 0/1 INFO :: Iteration: 71, Time: 1.053589e+00, dt: 2.143589e-02
2014-11-02 14:20:54,851 __main__ 0/1 INFO :: Iteration: 71, Time: 1.053589e+00, dt: 2.143589e-02
2014-11-02 14:20:55,814 __main__ 0/1 INFO :: Iteration: 81, Time: 1.267948e+00, dt: 2.357948e-02
2014-11-02 14:20:55,936 __main__ 0/1 INFO :: Iteration: 81, Time: 1.267948e+00, dt: 2.357948e-02
2014-11-02 14:20:56,002 __main__ 0/1 INFO :: Iteration: 81, Time: 1.267948e+00, dt: 2.357948e-02
2014-11-02 14:20:56,507 __main__ 0/1 INFO :: Iteration: 81, Time: 1.267948e+00, dt: 2.357948e-02
2014-11-02 14:20:57,449 __main__ 0/1 INFO :: Iteration: 91, Time: 1.503742e+00, dt: 2.593742e-02
2014-11-02 14:20:57,562 __main__ 0/1 INFO :: Iteration: 91, Time: 1.503742e+00, dt: 2.593742e-02
2014-11-02 14:20:57,668 __main__ 0/1 INFO :: Iteration: 91, Time: 1.503742e+00, dt: 2.593742e-02
2014-11-02 14:20:58,180 __main__ 0/1 INFO :: Iteration: 91, Time: 1.503742e+00, dt: 2.593742e-02
2014-11-02 14:20:59,098 __main__ 0/1 INFO :: Iteration: 101, Time: 1.763117e+00, dt: 2.853117e-02
2014-11-02 14:20:59,203 __main__ 0/1 INFO :: Iteration: 101, Time: 1.763117e+00, dt: 2.853117e-02
2014-11-02 14:20:59,322 __main__ 0/1 INFO :: Iteration: 101, Time: 1.763117e+00, dt: 2.853117e-02
2014-11-02 14:20:59,851 __main__ 0/1 INFO :: Iteration: 101, Time: 1.763117e+00, dt: 2.853117e-02
2014-11-02 14:21:00,726 __main__ 0/1 INFO :: Iteration: 111, Time: 2.048428e+00, dt: 3.138428e-02
2014-11-02 14:21:00,847 __main__ 0/1 INFO :: Iteration: 111, Time: 2.048428e+00, dt: 3.138428e-02
2014-11-02 14:21:00,962 __main__ 0/1 INFO :: Iteration: 111, Time: 2.048428e+00, dt: 3.138428e-02
2014-11-02 14:21:01,533 __main__ 0/1 INFO :: Iteration: 111, Time: 2.048428e+00, dt: 3.138428e-02
2014-11-02 14:21:02,365 __main__ 0/1 INFO :: Iteration: 121, Time: 2.362271e+00, dt: 3.452271e-02
2014-11-02 14:21:02,490 __main__ 0/1 INFO :: Iteration: 121, Time: 2.362271e+00, dt: 3.452271e-02
2014-11-02 14:21:02,610 __main__ 0/1 INFO :: Iteration: 121, Time: 2.362271e+00, dt: 3.452271e-02
2014-11-02 14:21:03,065 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:21:03,065 __main__ 0/1 INFO :: Run time: 20.103513
2014-11-02 14:21:03,065 __main__ 0/1 INFO :: Iterations: 120
Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 482, in process
    dset.resize(index+1, axis=0)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/dataset.py", line 280, in resize
    self.id.set_extent(size)
  File "h5d.pyx", line 269, in h5py.h5d.DatasetID.set_extent (h5py/h5d.c:3603)
ValueError: Unable to set extend dataset (Addr overflow, addr = 56622872, size=3136, eoa=55977688)
2014-11-02 14:21:03,176 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:21:03,176 __main__ 0/1 INFO :: Run time: 20.518945
2014-11-02 14:21:03,176 __main__ 0/1 INFO :: Iterations: 125
Traceback (most recent call last):
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 91, in make_fid
    fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
  File "h5f.pyx", line 71, in h5py.h5f.open (h5py/h5f.c:1797)
OSError: Unable to open file (Truncated file: eof = 55977688, sblock->base_addr = 0, stored_eoa = 58152920)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 455, in process
    file = self.get_file()
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 346, in get_file
    return h5py.File(str(self.current_path), 'a')
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 222, in __init__
    fid = make_fid(name, mode, userblock_size, fapl)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 93, in make_fid
    fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
  File "h5f.pyx", line 90, in h5py.h5f.create (h5py/h5f.c:1975)
OSError: Unable to create file (Unable to open file: name = '/home/ghanesh/dedalus/dedalus2/examples/rayleigh/rayleig2/rayleigh_benard/snapshots/snapshots_f1/snapshots_f1_p0.h5', errno = 17, error message = 'file exists', flags = 15, o_flags = c2)
2014-11-02 14:21:03,309 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:21:03,309 __main__ 0/1 INFO :: Run time: 20.718147
2014-11-02 14:21:03,309 __main__ 0/1 INFO :: Iterations: 125
Traceback (most recent call last):
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 91, in make_fid
    fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
  File "h5f.pyx", line 71, in h5py.h5f.open (h5py/h5f.c:1797)
OSError: Unable to open file (Truncated file: eof = 55977688, sblock->base_addr = 0, stored_eoa = 58152920)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 455, in process
    file = self.get_file()
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 346, in get_file
    return h5py.File(str(self.current_path), 'a')
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 222, in __init__
    fid = make_fid(name, mode, userblock_size, fapl)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 93, in make_fid
    fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
  File "h5f.pyx", line 90, in h5py.h5f.create (h5py/h5f.c:1975)
OSError: Unable to create file (Unable to open file: name = '/home/ghanesh/dedalus/dedalus2/examples/rayleigh/rayleig2/rayleigh_benard/snapshots/snapshots_f1/snapshots_f1_p0.h5', errno = 17, error message = 'file exists', flags = 15, o_flags = c2)
2014-11-02 14:21:03,531 __main__ 0/1 ERROR :: Exception raised, triggering end of main loop.
2014-11-02 14:21:03,531 __main__ 0/1 INFO :: Run time: 20.991463
2014-11-02 14:21:03,531 __main__ 0/1 INFO :: Iterations: 128
Traceback (most recent call last):
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 91, in make_fid
    fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
  File "h5f.pyx", line 71, in h5py.h5f.open (h5py/h5f.c:1797)
OSError: Unable to open file (Truncated file: eof = 55977688, sblock->base_addr = 0, stored_eoa = 58152920)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "rayleigh_benard.py", line 130, in <module>
    solver.step(dt)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/solvers.py", line 306, in step
    self.timestepper.step(self, dt, wall_time)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/pde/timesteppers.py", line 104, in step
    evaluator.evaluate_scheduled(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 94, in evaluate_scheduled
    self.evaluate_handlers(scheduled_handlers, wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 136, in evaluate_handlers
    handler.process(wall_time, sim_time, iteration)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 455, in process
    file = self.get_file()
  File "/home/ghanesh/dedalus/dedalus2/dedalus/src/dedalus2/dedalus2/data/evaluator.py", line 346, in get_file
    return h5py.File(str(self.current_path), 'a')
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 222, in __init__
    fid = make_fid(name, mode, userblock_size, fapl)
  File "/home/ghanesh/dedalus/dedalus2/dedalus/lib/python3.4/site-packages/h5py/_hl/files.py", line 93, in make_fid
    fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
  File "h5f.pyx", line 90, in h5py.h5f.create (h5py/h5f.c:1975)
OSError: Unable to create file (Unable to open file: name = '/home/ghanesh/dedalus/dedalus2/examples/rayleigh/rayleig2/rayleigh_benard/snapshots/snapshots_f1/snapshots_f1_p0.h5', errno = 17, error message = 'file exists', flags = 15, o_flags = c2)

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 32397 RUNNING AT localhost.localdomain
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

[Daniel Lecoanet]

Hi Ghanesh,

You can use PYTHONPATH to tell python where to search for matplotlib.

As for your problems running in parallel...  It looks like what's going on is that you're actually running the same job four times, instead of running one job using four processors.  I suspect that the crashes are due to different processors trying to write to the same file at the same time, since they're all doing the same thing.  I'm confused why this is happening, since the code is supposed to know to run in parallel automatically for 2D problems.  Does anyone else have any insight on what might be going on?

Daniel

[Keaton Burns]

Hi Ghanesh,

I’m not using it myself, but I came across these instructions online for building a scientific python 3.4 stack on CentOS:

https://edwards.sdsu.edu/research/installing-python3-4-and-the-scipy-stack-on-centos/

Hopefully starting from the “setup install for matplotlib”, using the python3 from the install script, will help you get a working matplotlib.  Based on the log you sent, it just looks like you’re missing freetype, and this post has manual instructions for building that.

As for the parallel issue: I think Dan’s right, and I think that means that the MPI global communicator being imported by mpi4py isn’t the same one that’s running the job. This can happen if the MPI that was used to compile mpi4py isn’t the same version that’s being used to dispatch the job.

To double check, try starting up python3 and printing “mpi4py.get_config()”.  This should list the associated MPI compilers, and you can check if they’re from the same MPI that you’re using for mpiexec.

-Keaton

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAJoYf%3DikPKsvQUOxAVWH0EdFD7X65to_Rc53mKf7ixT0OTiMQg%40mail.gmail.com.

[j s oishi]

Hi Ghanesh,

To add to what Keaton says, you may be able to just do

$ yum install freetype-devel

And then after running the activate script,

$ pip install matplotlib

Then your Dedalus install should be complete.

As for the mpi problem, do you have mpi installed via yum? You might try running

$ mpiexec -np 4 python3 script.py

And see if that works.

Jeff

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/94B15953-9B70-4BB0-82E6-B87F5C91BB95%40gmail.com.

[j s oishi]

Oh, also, I would not recommend using PYTHONPATH to add the matplotlib the system installed. That was likely for python2 while Dedalus uses python3

Jeff

[Ghanesh Narasimhan]

Thank you all for your valuable suggestions.
Finally, I was able to setup run the code and generate plots smoothly.

a)
Firstly, I reinstalled the python stack from the page  suggested by Keaton. This solved the matplotlib issue. The page doesn't install other dependencies like hdf5, h5py , nose, mercurial, docopt, of which I already installed few of them using install.sh.
Any dependency which was reported missing while running the code was debugged by installing the relevant missing dependency using pip

b)
Secondly, the mpi error was due to the mismatch in the mpiexec file between mpi4py and that which was used for dispatching the job. mpi4py.get_config() command was helpful in identifying the correct mpi libraries. 
After all this , by identifying the correct export paths for MPI_PATH, LD_LIBRARY_PATH, PYTHONPATH, FFTW_PATH, I was able to run the problems in  example folder without any error. Even MPI worked.
So, thanks to all for helping me out regarding the installation. Now , will try out setting up my problem.

c)
The only error that I am facing now is that whenever I run ipython, I get the following error,

Traceback (most recent call last):

  File "/usr/local/bin/ipython", line 7, in <module>
    from IPython import start_ipython
ImportError: cannot import name 'start_ipython'
This prevents me from trying out tutorials .
I am trying to debug it, but till now not successful. If someone knows please tell me how to debug it. But otherwise the code is working fine. All the example problems ran smoothly.

d)
And lastly, I have one more doubt regarding the boundary conditions.
I learnt from Daniel that in cylindrical coordinates we can only implement periodic boundary conditions along z direction. Is it the same case even in cartesian too, or any problem specific boundary conditions can be given in all three directions in cartesian coordinates ?

Thank you & regards,
Ghanesh

...

[Ben Brown]

Ghanesh

On Mon, Nov 3, 2014 at 12:38 PM, Ghanesh Narasimhan <ghan...@gmail.com> wrote:

d)
And lastly, I have one more doubt regarding the boundary conditions.
I learnt from Daniel that in cylindrical coordinates we can only implement periodic boundary conditions along z direction. Is it the same case even in cartesian too, or any problem specific boundary conditions can be given in all three directions in cartesian coordinates ?

This is true for Cartesian as well.  The only direction we can apply arbitrary boundary conditions is in the direction that we do the linear solve over (typically the direction that has the chebyshev expansion, and required to be that direction if chebyshevs are used), and currently this solve can only be done on one dimension in Dedalus.  We typically call this the vertical direction in the problem.

Some cleverness can lead to simple non-periodic boundary conditions in the horizontal directions for Cartesian problems, by enforcing symmetry to create an impenetrable sidewall boundary condition.  Daniel has the most experience with that, and some advances are coming that should make the general treatment much more straightforward (Keaton and others are leading a basis rewrite that will enable this).

Regards,

--Ben

 

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[Daniel Lecoanet]

To expand briefly on what Ben mentioned...  Right now, we can only impose interesting boundary conditions in one direction.  For cylindrical geometry, this would be the radial direction.  For Cartesian geometry, you can pick any direction, but we typically pick the vertical direction.  The other directions must be either periodic, or representable as a sin/cos basis.  If you use a sin/cos basis in the x direction, then the x velocity is zero at the boundaries and all other quantities' x-derivative is zero at the boundaries.  This allows us to impose stress-free boundary conditions in the horizontal directions for Cartesian geometry and in the vertical direction for cylindrical geometry.

Long-term, we are planning on being able to impose interesting boundary conditions in multiple directions, but this will take a bit of work.

Daniel

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/CAHqBLzwaOsLF76tMa2D26J4LBVgU4R3R1%3Deamr%3D_e492aBk0aQ%40mail.gmail.com.

[Ghanesh Narasimhan]

Thank you for clearing the doubts Ben and Daniel. And  the ipython error is solved and is working now. So there is no problem anymore.

...

[Ali Asad]

Hi Ganesh,

I think I am having the same problem while running the example code. (see my question: https://groups.google.com/g/dedalus-users/c/qEtoSHGRAMg )

It would be really kind if you could explain your solution a little more in detail.