Dedalus2 Install error

[Peng Deng]

Dear Dedalus users,

Due to the renewal of the HPC facility in my university, I need to re-install Dedalus2 in the new HPC.

I follow the custom conda installation and use the bash file conda_install_dedalus2.sh. 

The sub-environment dedalus2 could be installed, but when I use 'python3 -m dedalus test' to verify the installation, errors pop up. Those errors (see the attached screenshot) seem to relate to multi-thread issue.

Should some options in the bash file (conda_install_dedalus2.sh) be modified accordingly to resolve this issue?

Thanks for your help.

Best,

Peng 

[Calum Skene]

Hi Peng,

Can you try running the tests again with less workers. Something like

PYTEST_WORKERS=3 python3 -m dedalus test

You are currently using 256 workers which is maybe the cause of the issue (especially if on a login node).

Best,

Calum

[Peng Deng]

Hi Calum,

Thank you very much for your reply.

I tried 'PYTEST_WORKERS=3 python3 -m dedalus test', but the tests are still run with 256 workers, same errors pop up, see the attached screenshot.

Best,

Peng

[Calum Skene]

Hi Peng,

Ah okay, PYTEST_WORKERS must be a d3 thing. Can you try running the tests in a job with 4 cores or something small. Hopefully this runs better.

Best,

Calum

[Peng Deng]

Hi Calum,

I installed dedalus3 on the HPC facility in my university and found all the tests smoothly passed with the PYTEST_WORKERS.

Now, I am using dedalus3 to simulate quasi-geostrophic vorticity equation in a doubly periodic domain and I am a little confused with the tau method to enforce gauge condition in doubly periodic domain.

The equation I want to simulate is a nondimensional three-layer quasi-geostrophic potential vorticity equation, which reads as:

dt(q_1) + 2*dx(q_1) + [2*alpha/(alpha + 1)]*dx(psi_1) + HD(q_1) = -J(psi_1,q_1)

dt(q_2) + [2/(alpha+1)]*dx(q_2) + [(2-2alpha)/(alpha+1)]*dx(psi2) + HD(q_2) = -J(psi_2)

dt(q_3) + [-2/(alpha+1)]*(1 - slope)*dx(psi_3) + HD(q_3) + drag = -J(psi_3,q_3)

q1 = L(psi1) + (psi2 - psi1)

q2 = L(psi2) + (psi1 + psi3 - 2*psi2)

q3 = L(psi3) + (psi2 - psi3)

where HD denotes hyperdiffusion and drag is parameterized as a quadratic friction.

When I did the simulation in dedalus2, I use the condition 'nx ==0 & ny ==0' to avoid evolving the 'nx==0 & ny ==0' mode but keep this mode zero for both PV and streamfunction.

Now I want to add the tau terms in the equation and prescribe the 'integ(psi_1) = 0', 'integ(psi_2) = 0' and 'integ(psi_3) = 0'.  

Do you have any suggestions on how to add the tau terms in the QG PV equations above?

I attach the code for simulating the above QG PV equation in d2 and d3 respectively, although the tau terms in  d3 code is not added in the equation.

Best,

Peng