installation problems?

[Luke Sjulson]

hello,

I'm trying to run spyking circus on Ubuntu 14.04 using anaconda. I am getting an error that I think is related to me having installed some dependencies incorrectly. Could anyone give me some advice on how to fix this? Also, it recommends upgrading MPI - how do I do that?

thanks!

Luke

Starting spyking circus at Tue May 9 10:01:29 2017.

Command line call:

spyking-circus /probox_zpool/preprocessing/ADR20-9/ADR20-9_2017-05-03/DAT/DAT.dat --method fitting --cpu 2

##################################################################

##### Welcome to the SpyKING CIRCUS (0.5.6) #####

##### #####

##### Written by P.Yger and O.Marre #####

##################################################################

Steps : fitting

GPU detected : True

Number of CPU : 2/8

Number of GPU : 0

Parallel HDF5 : False

Shared memory : False [please consider upgrading MPI]

Hostfile : /home/luke/spyking-circus/circus.hosts

##################################################################

------------------------- Informations -------------------------

| Number of recorded channels : 141

| Number of analyzed channels : 120

| File format : RAW_BINARY

| Data type : int16

| Sampling rate : 20 kHz

| Duration of the recording : 2 min 30 s 400 ms

| Width of the templates : 2 ms

| Spatial radius considered : 100 um

| Threshold crossing : both

| Waveform alignment : True

| Matched filters : False

| Template Extraction : median-raw

| Overwrite : True

| Collect all spikes : False

| Smart Search : True

| Smart Selection : False

------------------------------------------------------------------

------------------------- Informations -------------------------

| Using only 2 out of 8 local CPUs available (-c to change)

------------------------------------------------------------------

Here comes the SpyKING CIRCUS using 2 CPUs and 959 templates...

0%| |[00:00<?, ?it/s]Traceback (most recent call last):

File "/opt/anaconda2/bin/spyking-circus-subtask", line 11, in <module>

load_entry_point('spyking-circus==0.5.6', 'console_scripts', 'spyking-circus-subtask')()

File "/opt/anaconda2/lib/python2.7/site-packages/circus/scripts/subtask.py", line 43, in main

circus.launch(task, filename, nb_cpu, nb_gpu, use_gpu)

File "/opt/anaconda2/lib/python2.7/site-packages/circus/__init__.py", line 21, in launch

module.main(params, nb_cpu, nb_gpu, use_gpu)

File "/opt/anaconda2/lib/python2.7/site-packages/circus/fitting.py", line 304, in main

b = templates.dot(sub_mat)

File "/opt/anaconda2/lib/python2.7/site-packages/scipy/sparse/base.py", line 302, in dot

return self * other

File "/opt/anaconda2/lib/python2.7/site-packages/scipy/sparse/base.py", line 405, in __mul__

raise ValueError('dimension mismatch')

ValueError: dimension mismatch

Traceback (most recent call last):

File "/opt/anaconda2/bin/spyking-circus-subtask", line 11, in <module>

load_entry_point('spyking-circus==0.5.6', 'console_scripts', 'spyking-circus-subtask')()

File "/opt/anaconda2/lib/python2.7/site-packages/circus/scripts/subtask.py", line 43, in main

circus.launch(task, filename, nb_cpu, nb_gpu, use_gpu)

File "/opt/anaconda2/lib/python2.7/site-packages/circus/__init__.py", line 21, in launch

module.main(params, nb_cpu, nb_gpu, use_gpu)

File "/opt/anaconda2/lib/python2.7/site-packages/circus/fitting.py", line 304, in main

b = templates.dot(sub_mat)

File "/opt/anaconda2/lib/python2.7/site-packages/scipy/sparse/base.py", line 302, in dot

return self * other

File "/opt/anaconda2/lib/python2.7/site-packages/scipy/sparse/base.py", line 405, in __mul__

raise ValueError('dimension mismatch')

ValueError: dimension mismatch

---------------------------- Error -----------------------------

| Step "fitting" failed!

------------------------------------------------------------------

Traceback (most recent call last):

File "/opt/anaconda2/bin/spyking-circus", line 11, in <module>

load_entry_point('spyking-circus==0.5.6', 'console_scripts', 'spyking-circus')()

File "/opt/anaconda2/lib/python2.7/site-packages/circus/scripts/launch.py", line 352, in main

subprocess.check_call(mpi_args)

File "/opt/anaconda2/lib/python2.7/subprocess.py", line 186, in check_call

raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '['mpiexec', '-np', '2', 'spyking-circus-subtask', 'fitting', '/probox_zpool/preprocessing/ADR20-9/ADR20-9_2017-05-03/DAT/DAT.dat', '2', '0', 'False']' returned non-zero exit status 1

Process exited with exit code 1

[Pierre Yger]

Dear Luke

I must admit that I don't really know where does your error comes from. Since it is happening in the fitting step, I'm assuming everything worked well before during filtering/clustering. Can you tell me what is the scipy/numpy versions you are using, and send me the log file if any? Meanwhile, feel free to try to upgrade numpy/scipy with conda, it can not hurt. Does the code works for other datasets, or do you always get such an error?

Regarding how to upgrade MPI, it depend how you installed it. You can install it from sources (see here https://sysads.co.uk/2014/05/24/install-open-mpi-1-8-ubuntu-14-04-13-10/), or maybe conda has a more recent version released. You could also use apt-get with Ubuntu, however, for 14.04, I'm not sure you have distribution packages recent enough: the default MPI implementation for Ubuntu is openmpi, and I think you need a version higher than 1.8 at least. The key point is to have a version (either of openmpi or mpich2) that will support shared memory: in your case, since I can see that you have a rather large dictionary of templates, it will reduce quite a lot the memory consumption, and you should be able to use more cores

Best

Pierre

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[Luke Sjulson]

hi Pierre,

I think I figured out the problem. I was having a different error before, so I upgraded some dependencies, and I think I did the clustering and fitting stages with different library versions. I'm not sure why that would create problems, but I ran the first four tasks all at once just now, and it worked fine.

thanks again,

Luke

Lucas L. Sjulson, MD, PhD

Research Assistant Professor

Departments of Psychiatry and Neuroscience and Physiology

NYU School of Medicine

450 E. 29th St., 9th floor

New York, NY 10016

cell: 646-528-9672

fax: 646-501-4529

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[Pierre Yger]

Great, good to hear!

Best

Pierre