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public:processing_at_juropa [2013-07-26 14:00] – Stefan Froehlich | public:processing_at_juropa [2015-08-10 15:11] – [Juropa decommissioned] Stefan Froehlich | ||
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- | ====== Notes on Processing at the Juropa | + | ===== Juropa |
+ | The information below is only for backup and some install info might still be useful to other people. | ||
+ | The new system is Jureca and you can find the info here:\\ | ||
+ | [[http:// | ||
- | This is going to be the Wiki page for the Lofar Software | + | ===== Installation and Processing on Juropa ====== |
- | the Juelich | + | Here will be some notes on the Juropa |
+ | Work in progress but useful anyhow. | ||
+ | The next section Using Juropa for LOFAR Processing contains | ||
- | Currently | + | ===== Using Juropa for LOFAR Processing ====== |
- | that is part of the Calibration | + | Here are the most recent information |
- | awimager causes problems but might be working | + | Last edit June 2014. |
- | (details | + | ==== Account ==== |
- | The software | + | First of all you need an account on the system. The Project leader is Matthias Hoeft and the Project ID is HTB00 (needed for registration). |
- | path of the install is | + | The following website contains all necessary links for allocating computing time in the Jülich Supercomputing Centre (JSC). |
+ | Click on the link "User Accounts for projects on JUQUEEN, JUROPA, | ||
+ | [[http:// | ||
+ | german version: | ||
+ | [[http:// | ||
+ | Get in contact with Matthias so he can sign your account application and initiate the next steps. | ||
+ | ==== Acquiring Data ==== | ||
+ | Take a look at this site on how to get the data from the LTA\\ | ||
+ | [[http:// | ||
+ | To download data from the web you need the full filename. You can look those up in the catalog\\ | ||
+ | [[http:// | ||
+ | The Juelich Http download server | ||
+ | [[https:// | ||
+ | For Sara\\ | ||
+ | [[https:// | ||
+ | \\ | ||
+ | The recommended way to copy data is via srm copy. For doing this you need a Grid Certificate and to Register | ||
+ | ==== Register with the Virtual Organization ==== | ||
+ | You can register with the Lofar VO here: | ||
+ | [[https:// | ||
- | /lustre/jhome9/lofar/zdv596/LOFAR-Release-1_14 | + | ==== Grid Certificate ==== |
+ | To get direct srm copy access to the LTA storage you need a Grid Certificate.\\ | ||
+ | Its best to ask around in your institute where to get and how to install such a certificate. | ||
+ | General information about german grid certificates can be found here:\\ | ||
+ | [[http:// | ||
+ | ==== SRM Copy from Juropa ==== | ||
+ | There are two possible ways to create proxies on Juropa. With the ltools and grid-proxy-init commands or with voms-proxy-init.\\ | ||
+ | The main difference is the authentication at the VO server. The voms-proxy-init can directly get a user role as input where as the grid-proxy-init can not. For grid-proxy-init the user roles are compared to a local file that is synchronized with the SARA server once per day. So you have to wait until the next day after registering with the Lofar VO in order to use your proxies.\\ | ||
+ | == grid-proxy-init == | ||
+ | To use the grid-proxies simple follow these steps:\\ | ||
+ | Store your private key in '' | ||
+ | Execute:\\ < | ||
+ | Store your signed certificate in '' | ||
+ | Then you have to generate a proxy. Simply source the script\\ | ||
+ | < | ||
+ | and then you can create your proxy\\ | ||
+ | < | ||
+ | Test data retrieval: | ||
+ | When copying data with the --jobfile option, keep in mind that there is a 30min cpu limit on the login node. Meaning your srmcp should be shorter that 30min.\\ | ||
+ | \\ | ||
+ | == voms-proxy-init == | ||
+ | To use voms-proxies handle your keys and certificate as above and source the script | ||
+ | < | ||
+ | Optional: Set proxy environment variable to custom location:\\ < | ||
+ | Generate a proxy:\\ < | ||
+ | Test data retrieval: | ||
+ | ==== LOFAR Software ==== | ||
+ | The LOFAR Software Framework is installed in the home directory of user htb003. You load the environment with | ||
+ | < | ||
+ | This loads Release version 2.1 (in the future probably always the latest release). You can also load a 2.3 version (env_lofar_2.3.sh).\\ | ||
+ | There is more software available: | ||
- | You can find the lofar software in " | + | * Casapy 4.2 -> env_casapy.sh |
- | The environment you need is loaded with the script " | + | * Karma -> |
+ | * losoto -> env_losoto.sh | ||
- | In addition you might need a copy of the measurement data | + | In addition you might need a copy of the measurement data\\ |
- | /lustre/jhome9/lofar/zdv596/dataCEP in your home directory and point to | + | /lustre/jhome17/htb00/htb003/dataCEP\\ |
- | it in a file .casarc (just contains:" | + | Put it in your home directory and point to it in a file .casarc (just contains:" |
[yourhome]/ | [yourhome]/ | ||
If you require access to the GlobalSkyModel database, there is a copy of | If you require access to the GlobalSkyModel database, there is a copy of | ||
the database from the CEP Cluster (hopefully) running on the Juropa | the database from the CEP Cluster (hopefully) running on the Juropa | ||
- | login node jj28l02. Access the databse " | + | login node juropa02. Access the databse " |
- | " | + | " |
- | + | \\ | |
- | How to keep the measurement and gsm data up to date and distributed has | + | |
- | to be discussed | + | |
You can now run and test the executables on the login node from | You can now run and test the executables on the login node from | ||
" | " | ||
Line 41: | Line 93: | ||
Basically you use two scripts. One to configure the job and one to setup | Basically you use two scripts. One to configure the job and one to setup | ||
the environment for your program and run it.\\ | the environment for your program and run it.\\ | ||
- | Job configuration is pretty basic right now because we can only utilize | + | Do not get confused by the use of comments '#' |
- | one node per job. Do not get confused by the use of comments '#' | + | |
'#' | '#' | ||
recognized from the Moab batch system.\\ | recognized from the Moab batch system.\\ | ||
Line 54: | Line 105: | ||
#MSUB -N Lofar-test | #MSUB -N Lofar-test | ||
# just the name | # just the name | ||
- | #MSUB -l nodes=1: | + | #MSUB -l nodes=1: |
#MSUB -l walltime=00: | #MSUB -l walltime=00: | ||
#MSUB -e error.txt | #MSUB -e error.txt | ||
Line 72: | Line 123: | ||
time will be booked.\\ | time will be booked.\\ | ||
The maximum walltime is 24h.\\ | The maximum walltime is 24h.\\ | ||
- | The number of nodes has to stay at 1 for the time being. You can | + | It is a good practice |
- | experiment with ppn (process per node) which is used for openmp enabled | + | |
- | programs.\\ | + | |
- | It is best to name the log files error and output with some job specific | + | |
parameters and maybe the date.\\ | parameters and maybe the date.\\ | ||
You can choose to have mails send to you about the status of your job. | You can choose to have mails send to you about the status of your job. | ||
- | Contents of ' | + | Contents of ' |
< | < | ||
#/bin/sh! | #/bin/sh! | ||
#start of jobscript | #start of jobscript | ||
- | export OMP_NUM_THREADS=8 | + | export OMP_NUM_THREADS=16 |
# | # | ||
# | # | ||
- | export | + | export PYTHONPATH=/ |
- | PYTHONPATH=/ | + | export PYTHONPATH=/ |
- | export | + | |
- | PYTHONPATH=/ | + | |
# | # | ||
- | export PATH=/ | + | export PATH=/ |
- | export | + | export PATH=/ |
- | PATH=/ | + | export PATH=/ |
- | export | + | |
- | PATH=/ | + | |
# | # | ||
- | export | + | export LD_LIBRARY_PATH=/ |
- | LD_LIBRARY_PATH=/ | + | export LD_LIBRARY_PATH=/ |
- | export | + | export LD_LIBRARY_PATH=/ |
- | LD_LIBRARY_PATH=/ | + | export LD_LIBRARY_PATH=/ |
- | export | + | |
- | LD_LIBRARY_PATH=/ | + | |
- | export | + | |
- | LD_LIBRARY_PATH=/ | + | |
# | # | ||
- | export LOFARROOT=/ | + | export LOFARROOT=/ |
# | # | ||
- | /lustre/jhome9/lofar/zdv596/ | + | module load gsl |
- | /lustre/jwork/lofar/zdv596/Pipeline_testdata/calibrator_pipeline/Observation64405 | + | module load GCC/4.6.3 |
- | -c | + | # |
- | /lustre/jhome9/lofar/zdv596/ | + | /lustre/jhome17/htb00/htb003/ |
- | --job calibrator_branch_regression | + | |
</ | </ | ||
Line 120: | Line 159: | ||
Example of Alexanders bbs test: | Example of Alexanders bbs test: | ||
/ | / | ||
- | -v -n -f L104244_SB200_uv.dppp.MS BBS.parset skymodel.parset | + | -v -n -f L104244_SB200_uv.dppp.MS BBS.parset skymodel.parset\\ |
One important remark for your working directory. Use the Filesystem | One important remark for your working directory. Use the Filesystem | ||
mounted under $WORK for your data and jobs.\\ | mounted under $WORK for your data and jobs.\\ | ||
Line 128: | Line 167: | ||
(scratch file system). No backup of files residing here. Files not used | (scratch file system). No backup of files residing here. Files not used | ||
for more than 28 days will be automatically deleted! | for more than 28 days will be automatically deleted! | ||
+ | ==== Jobs in parallel ==== | ||
+ | (this section has to be reedited because of a bug involving the PSI_WAIT parameter. for working multinoe compatible scripts as Bjoern for the moment. I will edit this section with the correct information after 16.6.14) | ||
+ | You can start one job for every independent piece of data. You can use your old scripts and the pipeline scripts but every subtask will be processed in serial on one node. So typically you only allocate one node for your jobs.\\ | ||
+ | To circumvent this, start the subprocesses in the python scripts in a different manner. Use the mpiexec command to start your subprocess. The Parastation MPI Demon will then allocate free resources to your subprocess when available. For this behavior the environment variable PSI_WAIT has to be set. This means you can allocate the partition you want to work on with more than one node. Run your script and whenever you use a subprocess call use mpiexec with number of processes equal to one (np=1).\\ | ||
+ | You can have up to 16 processes per node (eight cpus + smt mode). How many of these processes are allocated to your np=1 option depends on the number of threads you want to have for openMP. So for OMP_NUM_THREADS=4 you will be able to run 4 subprocesses on one node. With OMP_NUM_THREADS=16 one subprocess per node and with OMP_NUM_THREADS=1 you will have 16.\\ | ||
+ | As an example lets look at a part of a script from Andreas (run_NDPPPs.py): | ||
+ | The snippet shows the the subprocess call with subprocess.Popen and how their return is handled. What has to be executed is in the list of tupels " | ||
+ | < | ||
+ | while True: | ||
+ | while cmds and len(processes) < max_task: | ||
+ | task = cmds.pop() | ||
+ | print time.asctime()," | ||
+ | processes.append([Popen(task, | ||
+ | if waittime: | ||
+ | break | ||
+ | for p in processes: | ||
+ | if done(p[0]): | ||
+ | if success(p[0]): | ||
+ | os.remove(p[1]) | ||
+ | processes.remove(p) | ||
+ | else: | ||
+ | fail() | ||
+ | if not processes and not cmds: | ||
+ | break | ||
+ | else: | ||
+ | time.sleep(sleeptime) | ||
+ | </ | ||
+ | To use multiple nodes on Juropa the command that is passed to popen has to be changed in the following way. The first argument is the executable followed by the arguments. The argument for "/ | ||
+ | < | ||
+ | for task in cmds: | ||
+ | command = [" | ||
+ | print command | ||
+ | processes.append([Popen(command, | ||
- | If you want to try the awimager try another build directly | + | while True: |
- | directory / | + | for p in processes: |
- | There are some weird problems with pyrap and this version uses a | + | if done(p[0]): |
- | different compiler. The awimager seems to work but there are other | + | if success(p[0]): |
- | problems which extend has not been analyzed yet. | + | os.remove(p[1]) |
+ | | ||
+ | else: | ||
+ | print "Error in: ",p[1] | ||
+ | os.remove(p[1]) | ||
+ | | ||
+ | |||
+ | if not processes: | ||
+ | break | ||
+ | </ | ||
Line 140: | Line 221: | ||
Good luck and let me know of any problems and feel free to give some | Good luck and let me know of any problems and feel free to give some | ||
feedback. | feedback. | ||
+ | ===== Old installation guide (still useful information, | ||
+ | |||
+ | The following libraries with given versions are installed in the home of user htb003 on Juropa.\\ | ||
+ | / | ||
+ | |||
+ | ^ Library ^ Version ^ | ||
+ | | bison | 2.5 | | ||
+ | | blitz | 0.10 | | ||
+ | | boost | 1.44.0 | | ||
+ | | cmake | 2.8.5 | | ||
+ | | casacore | trunk | | ||
+ | | casarest | 8741 | | ||
+ | | cfitsio | 3240 | | ||
+ | | fftw | 3.2.2 | | ||
+ | | flex | 2.5.35 | | ||
+ | | hdf5 | 1.8.4 | | ||
+ | | libpng | 1.5.6 | | ||
+ | | libpqxx | 3.1 | | ||
+ | | log4cplus | 1.0.4 | | ||
+ | | matplotlib | 1.2.1 | | ||
+ | | m4 | 1.4.16 | | ||
+ | | monetdb python client | 11.15.7 | | ||
+ | | numpy | 1.7.1 | | ||
+ | | OpenBLAS | 0.2.5 | | ||
+ | | PostgreSQL | 9.1.2 | | ||
+ | | pyrap | trunk | | ||
+ | | python | 2.7.5 | | ||
+ | | scons | 1.3.0 | | ||
+ | | setuptools | 0.6c11 | | ||
+ | | wcslib | 4.4.4 | | ||
+ | | unittest-xml-reporting | 1.5.0 | | ||
+ | | pyfits | 3.1.2 | | ||
+ | | pywcs | 1.10.2 | | ||
+ | | scipy | 0.12.0 | | ||
+ | | argparse | 1.2.1 | | ||
+ | | libiberty | | | ||
+ | | LOFAR | 1.16 | | ||
+ | |||
+ | Additional software for post processing requested by users: | ||
+ | ^ Package ^ Version ^ | ||
+ | | SIP | 4.15.1 | | ||
+ | | PyQt4 | 4.10.3 | | ||
+ | | iPython | 1.1.0 | | ||
+ | | casapy | 41.0.24668| | ||
+ | |||
+ | ==== LTA Installation on Juropa ===== | ||
+ | |||
+ | The operating system is: | ||
+ | < | ||
+ | SUSE Linux Enterprise Server 11 (x86_64) | ||
+ | VERSION = 11 | ||
+ | PATCHLEVEL = 1 | ||
+ | </ | ||
+ | With kernel version: | ||
+ | < | ||
+ | Linux 2.6.32.59-0.3-default x86_64 GNU/Linux | ||
+ | </ | ||
+ | The current working installation is in: | ||
+ | < | ||
+ | / | ||
+ | </ | ||
+ | Some things have to be Changed in order to compile and run everything on Juropa. | ||
+ | |||
+ | ==== General Compile settings ==== | ||
+ | There are unresolved issues with older versions. Tests with gcc4.3.4 and gcc4.4.6 gave the error: | ||
+ | < | ||
+ | File " | ||
+ | return self._getDefValues (parmnamepattern) | ||
+ | TypeError: No to_python (by-value) converter found for C++ type: casa:: | ||
+ | </ | ||
+ | The compiler suite has to be changed to gcc4.6.3. You do this with the command: | ||
+ | < | ||
+ | module load GCC/4.6.3 | ||
+ | </ | ||
+ | You also have to load the gsl module | ||
+ | < | ||
+ | module load gsl | ||
+ | </ | ||
+ | |||
+ | Set environment variables: | ||
+ | < | ||
+ | export CC=/ | ||
+ | export CXX=/ | ||
+ | </ | ||
+ | |||
+ | Using gcc4.6.3 gives the error | ||
+ | < | ||
+ | File " | ||
+ | self._addcols (tdesc, dminfo, addtoparent) | ||
+ | TypeError: No registered converter was able to produce a C++ rvalue of type int from this Python object of type numpy.int32 | ||
+ | </ | ||
+ | This can be corrected by changing the order of the " | ||
+ | |||
+ | Change from: | ||
+ | < | ||
+ | from __future__ import with_statement | ||
+ | import sys | ||
+ | import shutil | ||
+ | import os | ||
+ | import subprocess | ||
+ | import copy | ||
+ | from lofarpipe.support.pipelinelogging import CatchLog4CPlus | ||
+ | from lofarpipe.support.pipelinelogging import log_time | ||
+ | from lofarpipe.support.utilities import patch_parset | ||
+ | from lofarpipe.support.utilities import catch_segfaults | ||
+ | from lofarpipe.support.lofarnode import | ||
+ | from lofarpipe.support.utilities import create_directory | ||
+ | from lofarpipe.support.data_map import DataMap | ||
+ | from lofarpipe.support.subprocessgroup import SubProcessGroup | ||
+ | |||
+ | import pyrap.tables as pt | ||
+ | </ | ||
+ | to | ||
+ | < | ||
+ | from __future__ import with_statement | ||
+ | import sys | ||
+ | import shutil | ||
+ | import os | ||
+ | import subprocess | ||
+ | import copy | ||
+ | import pyrap.tables as pt | ||
+ | from lofarpipe.support.pipelinelogging import CatchLog4CPlus | ||
+ | from lofarpipe.support.pipelinelogging import log_time | ||
+ | from lofarpipe.support.utilities import patch_parset | ||
+ | from lofarpipe.support.utilities import catch_segfaults | ||
+ | from lofarpipe.support.lofarnode import | ||
+ | from lofarpipe.support.utilities import create_directory | ||
+ | from lofarpipe.support.data_map import DataMap | ||
+ | from lofarpipe.support.subprocessgroup import SubProcessGroup | ||
+ | </ | ||
+ | |||
+ | ==== Libiberty ==== | ||
+ | The change of the compiler suite brings additional problems. The system paths change to custom locations which prevents the finding of the correct version of the library " | ||
+ | |||
+ | ==== PYRAP ==== | ||
+ | Pyrap will not compile because it will not find the glibc libraries as they are not in the standard location anymore. To correct this you have to edit the pyrap SConsript in pyrap/ | ||
+ | < | ||
+ | env = Environment(ENV = { ' | ||
+ | ' | ||
+ | }, | ||
+ | </ | ||
+ | to | ||
+ | < | ||
+ | env = Environment(ENV = os.environ, | ||
+ | </ | ||
+ | Note: you have to use the trunk version and not the latest release because otherwise pyrap tables wont work. | ||
+ | Also add the the compile option --enable-rpath. Use " | ||
+ | |||
+ | ==== FFTW ==== | ||
+ | For the fftw library you have to add the option " | ||
+ | |||
+ | ==== SCIPY ==== | ||
+ | For scipy add the environment variable UMFPACK=" | ||
+ | |||
+ | ==== Blitz ==== | ||
+ | Version 0.9 did not compile. Version 0.10 works fine. | ||
+ | |||
+ | ==== CMake ==== | ||
+ | Tried using the system installed CMake which is also version 2.8.5. There are Problems with some " | ||
+ | |||
+ | ==== Casacore ==== | ||
+ | Need to use the trunk version instead of release 1.5 for functionality. Using the buildscript options, Casacore is missing support for hdf5 which is needed for the final steps of the imaging pipeline. Added hdf5 support as well as OpenMP and Threads by hand in the ccmake interface. ToDo: add options to buildscript | ||
+ | |||
+ | ==== LOFAR ==== | ||
+ | The system installed libpng was hiding the selfcompiled version which lead to problems during program execution. The proper path to libpng library and include dir have to be set in cmake. Same goes for the selfcompiled libiberty. ToDo: add options in cmake.build file (at least for libpng since its part of standard installation).\\ | ||
+ | The variants file GNU.cmake has to be edited to set the path to the new compiler version | ||
+ | < | ||
+ | # GNU compiler suite | ||
+ | set(GNU_COMPILERS GNU_C GNU_CXX GNU_Fortran GNU_ASM) | ||
+ | set(GNU_C | ||
+ | set(GNU_CXX | ||
+ | set(GNU_Fortran | ||
+ | set(GNU_ASM | ||
+ | </ | ||
+ | |||
+ | ==== SSH support ==== | ||
+ | Logging into compute nodes via ssh is not permitted on the system. Subprocesses have to be started on the one rented compute for now via shell or mpiexec command. Distribution to multiple nodes is in the works. | ||
+ | |||
+ | lofarpipe/ | ||
+ | |||
+ | ==== File copy ==== | ||
+ | Since the Juropa cluster uses a shared filesystem every data should be (read: HAS to be) present at job start to not waste computing time. The login nodes are supposed to be used for job preparation and analysis afterwards. So we do not need to copy data to the working directory (quota is limited!). The change for that is in lofarpipe/ | ||
+ | |||
+ | === Imaging Pipeline === | ||
+ | Because the datacopy to the working directory will not be done automatically the data has to present in your working directory set in pipeline.cfg plus subfolder jobname. Somthing like working_dir/ | ||
+ | In lofarpipe/ | ||
+ | |||
+ | |||
+ | ==== GSM Database ==== | ||
+ | A local version of the GSM Database has to be used. At the moment it is running on Juropa02 but has to be restarted after downtimes or after the demon used up its 30min wallclock time. The database is in the home folder of user zdv596 and can be started with | ||
+ | < | ||
+ | cd / | ||
+ | monetdbd start gsm | ||
+ | monetdb start gsm | ||
+ | </ | ||
+ | monetdb is installed in / | ||
+ | How to install a local GSM Database take a look at this [[http:// | ||
+ | |||
+ | ==== gsmutils.py ==== | ||
+ | The changes made during release 1.14 (after initial release) break the functionality of the database access on Juropa. You can revert back to the initial release of 1.14 or use the fix mentioned below. The error is as follows: | ||
+ | < | ||
+ | ERROR: | ||
+ | !BATfetchjoin(tmpr_2277, | ||
+ | |||
+ | ERROR: | ||
+ | Traceback (most recent call last): | ||
+ | File "/ | ||
+ | _jobid, _jobhost, _jobport).run_with_stored_arguments()) | ||
+ | File "/ | ||
+ | returnvalue = self.run_with_logging(*self.arguments) | ||
+ | File "/ | ||
+ | return self.run(*args) | ||
+ | File "/ | ||
+ | monet_db_password, | ||
+ | TypeError: ' | ||
+ | </ | ||
+ | Bart Scheers provided a temporary fix for this issue. You need to change the configuration of your database. | ||
+ | < | ||
+ | Stop gsm database set nthreads property to 1: | ||
+ | |||
+ | monetdb stop gsm | ||
+ | monetdb set nthreads=1 gsm | ||
+ | monetdb start gsm | ||
+ | </ | ||
+ | |||
+ | ==== imager_prepare.py ==== | ||
+ | Prevent datacopy when working on local host only. No " | ||
+ | SVN diff for lofarpipe/ | ||
+ | < | ||
+ | Index: CEP/ | ||
+ | =================================================================== | ||
+ | --- CEP/ | ||
+ | +++ CEP/ | ||
+ | @@ -10,6 +10,7 @@ | ||
+ | | ||
+ | | ||
+ | | ||
+ | +import pyrap.tables as pt | ||
+ | from lofarpipe.support.pipelinelogging import CatchLog4CPlus | ||
+ | from lofarpipe.support.pipelinelogging import log_time | ||
+ | from lofarpipe.support.utilities import patch_parset | ||
+ | @@ -19,7 +20,7 @@ | ||
+ | from lofarpipe.support.data_map import DataMap | ||
+ | from lofarpipe.support.subprocessgroup import SubProcessGroup | ||
+ | |||
+ | -import pyrap.tables as pt | ||
+ | +#import pyrap.tables as pt | ||
+ | |||
+ | # Some constant settings for the recipe | ||
+ | | ||
+ | @@ -140,37 +141,44 @@ | ||
+ | if input_item.skip == True: | ||
+ | | ||
+ | |||
+ | - # construct copy command | ||
+ | - command = [" | ||
+ | - input_item.host, | ||
+ | - " | ||
+ | + | ||
+ | + | ||
+ | + | ||
+ | + # skip the copy if machine is the same (execution on localhost). | ||
+ | + # make sure data is in the correct directory. for now: working_dir/ | ||
+ | + if input_item.host != " | ||
+ | + | ||
+ | + # construct copy command | ||
+ | + | ||
+ | + | ||
+ | + " | ||
+ | |||
+ | - self.logger.debug(" | ||
+ | + | ||
+ | |||
+ | - # Spawn a subprocess and connect the pipes | ||
+ | - # The copy step is performed 720 at once in that case which might | ||
+ | - # saturate the cluster. | ||
+ | - copy_process = subprocess.Popen( | ||
+ | - command, | ||
+ | - stdin=subprocess.PIPE, | ||
+ | - stdout=subprocess.PIPE, | ||
+ | - stderr=subprocess.PIPE) | ||
+ | + # Spawn a subprocess and connect the pipes | ||
+ | + # The copy step is performed 720 at once in that case which might | ||
+ | + # saturate the cluster. | ||
+ | + | ||
+ | + | ||
+ | + | ||
+ | + | ||
+ | + | ||
+ | |||
+ | - # Wait for finish of copy inside the loop: enforce single tread | ||
+ | - # copy | ||
+ | - (stdoutdata, | ||
+ | + # Wait for finish of copy inside the loop: enforce single tread | ||
+ | + # copy | ||
+ | + | ||
+ | |||
+ | - exit_status = copy_process.returncode | ||
+ | + | ||
+ | |||
+ | #if copy failed log the missing file and update the skip fields | ||
+ | - if exit_status != 0: | ||
+ | - input_item.skip = True | ||
+ | - copied_item.skip = True | ||
+ | - self.logger.warning( | ||
+ | + if exit_status != 0: | ||
+ | + | ||
+ | + | ||
+ | + | ||
+ | " | ||
+ | - self.logger.warning(stderrdata) | ||
+ | + | ||
+ | |||
+ | - self.logger.debug(stdoutdata) | ||
+ | + | ||
+ | |||
+ | | ||
+ | |||
+ | @@ -298,7 +306,8 @@ | ||
+ | |||
+ | # construct copy command | ||
+ | | ||
+ | - command = [rficonsole_executable, | ||
+ | + command = [rficonsole_executable, | ||
+ | + ## " | ||
+ | | ||
+ | | ||
+ | " | ||
+ | </ | ||
+ | ==== remotecommand.py ==== | ||
+ | Extra Path variable for remote systems where python is not installed in the same place as on the master node.\\ | ||
+ | Prevent ssh commands entirely as they are not supported on Juropa. Just a switch for localhost. SVN diff: | ||
+ | < | ||
+ | Index: CEP/ | ||
+ | =================================================================== | ||
+ | --- CEP/ | ||
+ | +++ CEP/ | ||
+ | @@ -111,13 +111,29 @@ | ||
+ | | ||
+ | | ||
+ | |||
+ | +def run_via_local(logger, | ||
+ | + commandstring = ["/ | ||
+ | + for arg in arguments: | ||
+ | + command = command + " " + str(arg) | ||
+ | + commandstring.append(command) | ||
+ | + process = spawn_process(commandstring, | ||
+ | + process.kill = lambda : os.kill(process.pid, | ||
+ | + return process | ||
+ | + | ||
+ | def run_via_ssh(logger, | ||
+ | """ | ||
+ | | ||
+ | |||
+ | We return a Popen object pointing at the SSH session, to which we add a | ||
+ | kill method for shutting down the connection if required. | ||
+ | + | ||
+ | + hack/ | ||
+ | + if host is localhost run without ssh | ||
+ | + /hack | ||
+ | """ | ||
+ | + if host == " | ||
+ | + logger.debug(" | ||
+ | + return run_via_local(logger, | ||
+ | | ||
+ | | ||
+ | |||
+ | @@ -214,6 +230,7 @@ | ||
+ | | ||
+ | | ||
+ | { | ||
+ | + " | ||
+ | " | ||
+ | " | ||
+ | }, | ||
+ | </ | ||
+ | ==== copier.py ==== | ||
+ | The copy process of the Intrument files used in the target pipeline has to be changed because rsync is not supported between nodes. Change to a simple copy command.\\ | ||
+ | recipes/ | ||
+ | < | ||
+ | 53,56c53 | ||
+ | < if source_node==" | ||
+ | < | ||
+ | < else: | ||
+ | < | ||
+ | --- | ||
+ | > | ||
+ | </ | ||
+ | ==== parset.py ==== | ||
+ | Changed the " | ||
+ | Should maybe be changed to the working directory?! | ||
- | on holidays for one week... after that more updates |