Hi,

Our commit 94f4ea3 should have fixed this error, but some people still
report this error. So I made another commit 86324b2 with further workaround.
When this workaround is triggered, debug information is printed.
When this happened, please let me know.

Best regards,

Takanori Nakane

> Somnath,
>
> Sorry I have lost my password to the forums and have to email you from
> here.  If this helps please post it to the forums.
>
> So I have had the same exact problem in my 2D class job and tried solving
> it the same ways with no success.
>
> I use two separate computers to run my jobs.  On at home and one at work.
> These both connect to the same server however, occasionally I get this MPI
> error you get.  Now before in relion 2.1 there was no
> "Backprojector::se... " message but now with Relion 3 there is.
>
> To fix this I use the   ps x    command (on both computers) and kill all
> the jobs running.  I did this just this morning and sure enough, there was
> a job there that wasn't on my terminal from home (why I do not know). I
> after running the ps x command I then killed the jon and BAM.  Job is
> running smoothly.
>
> Again I am not sure this will help but out 2 problems seemed almost
> identical and this is how I solved it.  Just ps x from every computer that
> tryed running that job and kill it.
>
> Good luck
>
> Kako
> PS.  I am still just a super beginner so hope this made sense.  I still
> don't know the right way to word things.
>
> 。・゜・。。・゜・。。・゜・。。・゜・。・゜・。。・゜・。。・゜・。。・゜・。
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> 。・゜・。。・゜・。。・゜・。。・゜・。・゜・。。・゜・。。・゜・。。・゜・。
> 。・゜・。。・゜・。。・゜・。。・゜・。・゜・。。・゜・。。・゜・。。・゜・。
> 。・゜・。。・゜・。。・゜・。。・゜・。・゜・。。・゜・。。・゜・。。・゜・。
> 。・゜・。。・゜・。。・゜・。。・゜・。・゜・。。・゜・。。・゜・。。・゜・。
> 。・゜・。。・゜・。。・゜・。。・゜・。・゜・。。・゜・。。・゜・。。・゜・。
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>
> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
> On Sunday, 11 November 2018 22:44, Somnath Dutta <[log in to unmask]>
> wrote:
>
>> Hi,
>>
>> I just did. But same error.
>>
>> Best,
>> SD
>>
>> On Sun, Nov 11, 2018 at 7:10 PM Sayan Bhakta <[log in to unmask]>
>> wrote:
>>
>>> Hi,
>>> Just to clarify...
>>> Have you tried with the same command with
>>>
>>> mpirun -np
>>>
>>> instead of
>>>
>>> mpirun --np
>>>
>>> ?
>>>
>>> On Sun 11 Nov, 2018, 17:36 Somnath Dutta <[log in to unmask]
>>> wrote:
>>>
>>>> Dear All,
>>>>
>>>> I am trying run 2D classification using Relion 2.1. I have a data set
>>>> 300k particles with box size 160.  I am getting an error message
>>>>
>>>> + WARNING: Changing psi sampling rate (before oversampling) to 11.25
>>>> degrees, for more efficient GPU calculations
>>>>  Estimating initial noise spectra
>>>> 1.52/1.72 min
>>>> ....................................................~~(,_,">ERROR: ]
>>>> Backprojector::set2DSlice%%ERROR: Dimension of the data array should
>>>> be 2 or 3
>>>> File: /data/tarfiles/relion-master/src/backprojector.h line: 201
>>>> --------------------------------------------------------------------------
>>>> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
>>>> with errorcode 1.
>>>>
>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>> You may or may not see output from other processes, depending on
>>>> exactly when Open MPI kills them.
>>>> --------------------------------------------------------------------------
>>>>
>>>> We have never seen this error before at least RELION 2.1. We have
>>>> re-extracted the images a couple of time but unfortunately getting
>>>> same error. We separated data set into three halves (100k each) but we
>>>> are getting same error.
>>>>
>>>> We went back to our another project folder where that 2D
>>>> classification job ran successfully one week ago. We tried same
>>>> command but getting same error.
>>>>
>>>> I am using the following command
>>>> openmpi-3.1.0/bin/mpirun --np 3 relion_refine_mpi --o
>>>> Class2D/job063/run_02 --i Extract/job062/particles.star
>>>> --dont_combine_weights_via_disc --pool 3 --ctf --iter 25 --tau2_fudge
>>>> 2 --particle_diameter 90 --K 40 --flatten_solvent --zero_mask
>>>> --oversampling 1 --psi_step 12 --offset_range 5 --offset_step 2
>>>> --dont_check_norm --scale --j 4 --gpu --maxsig 2000 --firstiter_cc
>>>>
>>>> I have tried myself to resolve this problem, but I can't figure it out
>>>> what is the problem. Any help would be greatly appreciated.
>>>>
>>>> Best,
>>>> Somnath
>>>>
>>>> ---------------------------------------------------------------
>>>>
>>>> To unsubscribe from the CCPEM list, click the following link:
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>>
>> --
>> Dr. Somnath Dutta.
>> Assistant Professor
>> Molecular Biophysics Unit
>> Division of Biological Sciences
>> Indian Institute of Science
>> Bangalore - 560012, INDIA
>>
>> ---------------------------------------------------------------
>>
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