Comments (5)
I added some print statements to Ingram_inversion.py and get very clear where this it stalls when running from dask.distributed import Client, as_completed
.
I have added:
print ('ifgram_inversion: FROM DASK.DISTRIBUTED IMPORT CLIENT'); sys.stdout.flush()
from dask.distributed import Client, as_completed
print ('ifgram_inversion: FROM DASK.DISTRIBUTED IMPORT CLIENT DONE'); sys.stdout.flush()
# dask_jobqueue is needed for HPC.
# PBSCluster (similar to LSFCluster) should also work out of the box
print ('ifgram_inversion: FROM DASK_JOBQUEUE IMPORT LSFCLUSTER'); sys.stdout.flush()
from dask_jobqueue import LSFCluster
print ('ifgram_inversion: FROM DASK_JOBQUEUE IMPORT LSFCLUSTER DONE'); sys.stdout.flush()
The out put is:
******************** step - invert_network ********************
ifgram_inversion.py /projects/scratch/insarlab/famelung/unittestGalapagosSenDT128/mintpy/inputs/ifgramStack.h5 -t /projects/scratch/insarlab/famelung/unittestGalapagosSenDT128/mintpy/smallbaselineApp.cfg --update
--------------------------------------------------
update mode: ON
1) NOT ALL output files found: ['timeseries.h5', 'temporalCoherence.h5'].
run or skip: run.
-------------------------------------------------------------------------------
least-squares solution with L2 min-norm on: deformation velocity
minimum redundancy: 1.0
weight function: var
mask: no
-------------------------------------------------------------------------------
number of interferograms: 20
number of acquisitions : 7
number of lines : 833
number of columns : 1364
reference pixel in y/x: (455, 842) from dataset: unwrapPhase
ifgram_inversion run check: IN FUNCTION IFGRAM_INVERSION
ifgram_inversion: FROM DASK.DISTRIBUTED IMPORT CLIENT
from mintpy.
Another hint could be some warnings that come up when running from the shell (without bsub). But it also shows up in the working setup.
******************** step - invert_network ********************
ifgram_inversion.py /projects/scratch/insarlab/famelung/unittestGalapagosSenDT128/mintpy/inputs/ifgramStack.h5 -t /projects/scratch/insarlab/famelung/unittestGalapagosSenDT128/mintpy/smallbaselineApp.cfg --update
--------------------------------------------------
update mode: ON
1) NOT ALL output files found: ['timeseries.h5', 'temporalCoherence.h5'].
run or skip: run.
-------------------------------------------------------------------------------
least-squares solution with L2 min-norm on: deformation velocity
minimum redundancy: 1.0
weight function: var
mask: no
-------------------------------------------------------------------------------
number of interferograms: 20
number of acquisitions : 7
number of lines : 833
number of columns : 1364
reference pixel in y/x: (455, 842) from dataset: unwrapPhase
ifgram_inversion run check: IN FUNCTION IFGRAM_INVERSION
ifgram_inversion: FROM DASK.DISTRIBUTED IMPORT CLIENT
ifgram_inversion: FROM DASK.DISTRIBUTED IMPORT CLIENT DONE
ifgram_inversion: FROM DASK_JOBQUEUE IMPORT LSFCLUSTER
/nethome/famelung/test/operations/rsmas_insar/3rdparty/miniconda3/lib/python3.7/site-packages/dask_jobqueue/config.py:12: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
defaults = yaml.load(f)
ifgram_inversion: FROM DASK_JOBQUEUE IMPORT LSFCLUSTER DONE
/nethome/famelung/test/operations/rsmas_insar/3rdparty/miniconda3/lib/python3.7/site-packages/distributed/deploy/local.py:138: UserWarning: diagnostics_port has been deprecated. Please use `dashboard_address=` instead
"diagnostics_port has been deprecated. "
/nethome/famelung/test/operations/rsmas_insar/3rdparty/miniconda3/lib/python3.7/site-packages/distributed/bokeh/core.py:74: UserWarning:
Port 8787 is already in use.
Perhaps you already have a cluster running?
Hosting the diagnostics dashboard on a random port instead.
warnings.warn("\n" + msg)
JOB COMMAND CALLED FROM PYTHON: #!/bin/bash
#BSUB -J mintpy_bee
#BSUB -q general
#BSUB -P insarlab
#BSUB -n 2
#BSUB -R "span[hosts=1]"
#BSUB -M 2000
#BSUB -W 00:30
#BSUB -R "rusage[mem=2500]"
#BSUB -o worker_mintpy.%J.o
#BSUB -e worker_mintpy.%J.e
JOB_ID=${LSB_JOBID%.*}
/nethome/famelung/test/operations/rsmas_insar/3rdparty/miniconda3/bin/python3 -m distributed.cli.dask_worker tcp://10.11.1.13:34913 --nthreads 2 --memory-limit 2.00GB --name mintpy_bee--${JOB_ID}-- --death-timeout 60 --interface ib0
0 [0, 0, 34, 833]
1 [34, 0, 68, 833]
...
from mintpy.
When I use the old (test1) conda environment it works fine. So I tried to recreate this environment using pip. I did pip3 freeze > requirements_test1.txt
in the old environment and pip3 install -r requirements_test1.txt
to recreate exactly this environment but I get lots of errors:
ERROR: Could not find a version that satisfies the requirement basemap==1.2.0
ERROR: Could not find a version that satisfies the requirement conda==4.6.14;
No matching distribution found for GDAL==2.4.1;
Also for pygrib and pykml. I tried removing some of the requirements but error kept coming and then I gave up.
from mintpy.
The next thing I tried is to recreate the working environment using exactly the
cd setup
rm -rf ../3rdparty/miniconda3
miniconda_version=Miniconda3-4.5.12-Linux-x86_64.sh
./$miniconda_version -b -p ../3rdparty/miniconda3
cp condarc ../3rdparty/miniconda3/.condarc
../3rdparty/miniconda3/bin/conda install isce2 -c piyushrpt --yes
../3rdparty/miniconda3/bin/conda install --yes --file /nethome/famelung/test/test1/rsmas_insar/sources/PySAR/docs/conda.txt
../3rdparty/miniconda3/bin/conda install --yes --file /nethome/famelung/test/test1/rsmas_insar/setup/conda.txt
../3rdparty/miniconda3/bin/pip install --upgrade pip
../3rdparty/miniconda3/bin/pip install opencv-python
../3rdparty/miniconda3/bin/pip install geocoder
../3rdparty/miniconda3/bin/pip install git+https://github.com/tylere/pykml.git
(Note that the old conda.txt misses 2 entires:
diff conda.txt /nethome/famelung/test/operations/rsmas_insar/setup/conda.txt
4a5,6
> bokeh
> qt
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resolved by using LocalCluster
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