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public:processing_at_juropa [2013-09-05 09:24] – Stefan Froehlich | public:processing_at_juropa [2017-03-08 15:27] (current) – external edit 127.0.0.1 | ||
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+ | ===== Juropa decommissioned ===== | ||
+ | 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:// | ||
+ | |||
===== Installation and Processing on Juropa ====== | ===== Installation and Processing on Juropa ====== | ||
Here will be some notes on the Juropa installation and how to use the software on Juropa at the Juelich Supercomuting Centre.\\ | Here will be some notes on the Juropa installation and how to use the software on Juropa at the Juelich Supercomuting Centre.\\ | ||
- | Not finished yet but useful anyhow. | + | Work in progress |
+ | The next section Using Juropa for LOFAR Processing contains the information you need to use the system as of May 2014. The sections below these up to date information are kept for archiving purpose (still useful). | ||
- | ===== LTA Pipeline Environment Libraries | + | ===== Using Juropa for LOFAR Processing ====== |
+ | Here are the most recent information on how to make use of Juropa for LOFAR Processing. | ||
+ | Last edit June 2014. | ||
+ | ==== Account ==== | ||
+ | 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). | ||
+ | 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 is here\\ | ||
+ | [[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 in the Virtual Organization (VO) as a Lofar User. | ||
+ | ==== Register with the Virtual Organization | ||
+ | You can register with the Lofar VO here: | ||
+ | [[https:// | ||
- | The following libraries | + | ==== 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: | ||
+ | |||
+ | * Casapy 4.2 -> env_casapy.sh | ||
+ | * Karma -> | ||
+ | * losoto -> env_losoto.sh | ||
+ | |||
+ | In addition you might need a copy of the measurement data\\ | ||
+ | / | ||
+ | Put it in your home directory | ||
+ | [yourhome]/ | ||
+ | |||
+ | If you require access to the GlobalSkyModel database, there is a copy of | ||
+ | the database from the CEP Cluster (hopefully) running | ||
+ | login node juropa02. Access the databse " | ||
+ | " | ||
+ | \\ | ||
+ | You can now run and test the executables on the login node from | ||
+ | " | ||
+ | in " | ||
+ | |||
+ | To run your jobs on the compute nodes you first have to setup and submit | ||
+ | a job via the batch system. A detailed description can be found on the | ||
+ | Juropa homepage | ||
+ | ' | ||
+ | |||
+ | Here is a simple example of the procedure. | ||
+ | Basically you use two scripts. One to configure the job and one to setup | ||
+ | the environment | ||
+ | Do not get confused by the use of comments '#' | ||
+ | '#' | ||
+ | recognized from the Moab batch system.\\ | ||
+ | You submit the job with the command "msub [yourscript]" | ||
+ | status with "showq -u ' | ||
+ | try the " | ||
+ | |||
+ | Contents of ' | ||
+ | < | ||
+ | #!/bin/bash -x | ||
+ | #MSUB -N Lofar-test | ||
+ | # just the name | ||
+ | #MSUB -l nodes=1: | ||
+ | #MSUB -l walltime=00: | ||
+ | #MSUB -e error.txt | ||
+ | # if keyword omitted : default is submitting directory | ||
+ | #MSUB -o output.txt | ||
+ | # if keyword omitted : default is submitting directory | ||
+ | #MSUB -M your@mail.de | ||
+ | # | ||
+ | #MSUB -m eab | ||
+ | #send mail on end, abort, begin | ||
+ | ./ | ||
+ | </ | ||
+ | |||
+ | The walltime is the time your job will be running on the machine. If it | ||
+ | is to low and the job is not finished it will be killed. Is it to high | ||
+ | your job might have to wait longer in queue but only the real computing | ||
+ | time will be booked.\\ | ||
+ | The maximum walltime is 24h.\\ | ||
+ | It is a good practice to name the log files error and output with some job specific | ||
+ | parameters and maybe the date.\\ | ||
+ | You can choose to have mails send to you about the status of your job. | ||
+ | |||
+ | |||
+ | Contents of ' | ||
+ | < | ||
+ | #/bin/sh! | ||
+ | #start of jobscript | ||
+ | export OMP_NUM_THREADS=16 | ||
+ | # | ||
+ | # | ||
+ | export PYTHONPATH=/ | ||
+ | export PYTHONPATH=/ | ||
+ | # | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | # | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | # | ||
+ | export LOFARROOT=/ | ||
+ | # | ||
+ | module load gsl | ||
+ | module load GCC/4.6.3 | ||
+ | # | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | Simply replace the pipeline call with the command you want to run in | ||
+ | your job. | ||
+ | Example of Alexanders bbs test: | ||
+ | / | ||
+ | -v -n -f L104244_SB200_uv.dppp.MS BBS.parset skymodel.parset\\ | ||
+ | One important remark for your working directory. Use the Filesystem | ||
+ | mounted under $WORK for your data and jobs.\\ | ||
+ | From the Juropa home page:\\ | ||
+ | $WORK\\ | ||
+ | File system for large temporary files with high I/O bandwidth demands | ||
+ | (scratch file system). No backup of files residing here. Files not used | ||
+ | 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, | ||
+ | |||
+ | while True: | ||
+ | for p in processes: | ||
+ | if done(p[0]): | ||
+ | if success(p[0]): | ||
+ | os.remove(p[1]) | ||
+ | processes.remove(p) | ||
+ | else: | ||
+ | print "Error in: ", | ||
+ | os.remove(p[1]) | ||
+ | processes.remove(p) | ||
+ | |||
+ | if not processes: | ||
+ | break | ||
+ | </ | ||
+ | |||
+ | |||
+ | I hope these information are sufficient for some first tests and | ||
+ | experiments.\\ | ||
+ | Good luck and let me know of any problems and feel free to give some | ||
+ | feedback. | ||
+ | ===== Old installation guide (still useful information, | ||
+ | |||
+ | The following libraries with given versions are installed in the home of user htb003 | ||
+ | / | ||
^ Library ^ Version ^ | ^ Library ^ Version ^ | ||
Line 38: | Line 257: | ||
| argparse | 1.2.1 | | | argparse | 1.2.1 | | ||
| libiberty | | | | libiberty | | | ||
- | | LOFAR | 1.14 | | + | | 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 | + | ==== LTA Installation on Juropa ===== |
The operating system is: | The operating system is: | ||
Line 54: | Line 280: | ||
The current working installation is in: | The current working installation is in: | ||
< | < | ||
- | / | + | / |
</ | </ | ||
Some things have to be Changed in order to compile and run everything on Juropa. | Some things have to be Changed in order to compile and run everything on Juropa. | ||
Line 86: | Line 312: | ||
TypeError: No registered converter was able to produce a C++ rvalue of type int from this Python object of type numpy.int32 | 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 " | + | This can be corrected by changing the order of the " |
Change from: | Change from: | ||
Line 194: | Line 420: | ||
==== gsmutils.py ==== | ==== gsmutils.py ==== | ||
- | The changes made during release 1.14 (after initial release) break the functionality of the database access on Juropa. | + | The changes made during release 1.14 (after initial release) break the functionality of the database access on Juropa. |
< | < | ||
ERROR: | ERROR: | ||
Line 210: | Line 436: | ||
monet_db_password, | monet_db_password, | ||
TypeError: ' | 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 | ||
</ | </ | ||
Line 220: | Line 454: | ||
--- CEP/ | --- CEP/ | ||
+++ CEP/ | +++ CEP/ | ||
- | @@ -140,37 +140,44 @@ | + | @@ -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: | if input_item.skip == True: | ||
| | ||
Line 288: | Line 539: | ||
| | ||
- | @@ -298,7 +305,8 @@ | + | @@ -298,7 +306,8 @@ |
# construct copy command | # construct copy command | ||
Line 298: | Line 549: | ||
| | ||
" | " | ||
- | |||
</ | </ | ||
Line 349: | Line 599: | ||
</ | </ | ||
- | + | ==== copier.py ==== | |
- | ====== Notes on Processing at the Juropa Cluster ====== | + | The copy process of the Intrument files used in the target |
- | + | recipes/nodes/copier.py | |
- | This is going to be the Wiki page for the Lofar Software installation at | + | |
- | the Juelich Supercomupting Centre.I will update this page as the installation progresses. | + | |
- | + | ||
- | ==== 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:// | + | |
- | If you want to do a direct srm copy you need a Grid Certificate. | + | |
- | + | ||
- | ==== German Grid Certificate ==== | + | |
- | To get direct srm copy access to the LTA storage you need a Grid Certificate.\\ | + | |
- | [[http://dgi-2.d-grid.de/ | + | |
- | + | ||
- | ==== SRM Copy from Juropa ==== | + | |
- | You need to load the ltools module and execute the given command to activate the environment to use " | + | |
< | < | ||
- | module load ltools | + | 53,56c53 |
- | . / | + | < if source_node==" |
+ | < | ||
+ | < | ||
+ | < | ||
+ | --- | ||
+ | > | ||
</ | </ | ||
- | Follow this Walkthrough to generate a proxy for your srm download | ||
- | [[http:// | ||
- | |||
- | ==== Running the Software ==== | ||
- | (already outdated, will get updates when Lofar v1.16 is installed (week of 2.9.13 maybe?!))\\ | ||
- | Currently the software is beeing tested on the Juropa system. Everything | ||
- | that is part of the Calibration and the Target Pipeline is working. The | ||
- | awimager causes problems but might be working in an experimental build | ||
- | (details at the end).\\ | ||
- | The software is available in the home directory of user zdv596. The root | ||
- | path of the install is | ||
- | |||
- | / | ||
- | |||
- | You can find the lofar software in " | ||
- | The environment you need is loaded with the script " | ||
- | |||
- | In addition you might need a copy of the measurement data | ||
- | / | ||
- | it in a file .casarc (just contains:" | ||
- | [yourhome]/ | ||
- | |||
- | If you require access to the GlobalSkyModel database, there is a copy of | ||
- | the database from the CEP Cluster (hopefully) running on the Juropa | ||
- | login node jj28l02. 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 | ||
- | " | ||
- | in " | ||
- | |||
- | To run your jobs on the compute nodes you first have to setup and submit | ||
- | a job via the batch system. A detailed description can be found on the | ||
- | Juropa homepage | ||
- | ' | ||
- | |||
- | Here is a simple example of the procedure. | ||
- | Basically you use two scripts. One to configure the job and one to setup | ||
- | the environment for your program and run it.\\ | ||
- | Job configuration is pretty basic right now because we can only utilize | ||
- | one node per job. Do not get confused by the use of comments '#' | ||
- | '#' | ||
- | recognized from the Moab batch system.\\ | ||
- | You submit the job with the command "msub [yourscript]" | ||
- | status with "showq -u ' | ||
- | try the " | ||
- | |||
- | Contents of ' | ||
- | < | ||
- | #!/bin/bash -x | ||
- | #MSUB -N Lofar-test | ||
- | # just the name | ||
- | #MSUB -l nodes=1: | ||
- | #MSUB -l walltime=00: | ||
- | #MSUB -e error.txt | ||
- | # if keyword omitted : default is submitting directory | ||
- | #MSUB -o output.txt | ||
- | # if keyword omitted : default is submitting directory | ||
- | #MSUB -M your@mail.de | ||
- | #Mailadress | ||
- | #MSUB -m eab | ||
- | #send mail on end, abort, begin | ||
- | ./ | ||
- | </ | ||
- | |||
- | The walltime is the time your job will be running on the machine. If it | ||
- | is to low and the job is not finished it will be killed. Is it to high | ||
- | your job might have to wait longer in queue but only the real computing | ||
- | time will be booked.\\ | ||
- | The maximum walltime is 24h.\\ | ||
- | The number of nodes has to stay at 1 for the time being. You can | ||
- | 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.\\ | ||
- | You can choose to have mails send to you about the status of your job. | ||
- | |||
- | |||
- | Contents of ' | ||
- | < | ||
- | #/bin/sh! | ||
- | #start of jobscript | ||
- | export OMP_NUM_THREADS=8 | ||
- | # | ||
- | # | ||
- | export | ||
- | PYTHONPATH=/ | ||
- | export | ||
- | PYTHONPATH=/ | ||
- | # | ||
- | export PATH=/ | ||
- | export | ||
- | PATH=/ | ||
- | export | ||
- | PATH=/ | ||
- | # | ||
- | export | ||
- | LD_LIBRARY_PATH=/ | ||
- | export | ||
- | LD_LIBRARY_PATH=/ | ||
- | export | ||
- | LD_LIBRARY_PATH=/ | ||
- | export | ||
- | LD_LIBRARY_PATH=/ | ||
- | # | ||
- | export LOFARROOT=/ | ||
- | # | ||
- | / | ||
- | / | ||
- | -c | ||
- | / | ||
- | --job calibrator_branch_regression -d | ||
- | </ | ||
- | |||
- | Simply replace the pipeline call with the command you want to run in | ||
- | your job. | ||
- | Example of Alexanders bbs test: | ||
- | / | ||
- | -v -n -f L104244_SB200_uv.dppp.MS BBS.parset skymodel.parset | ||
- | One important remark for your working directory. Use the Filesystem | ||
- | mounted under $WORK for your data and jobs.\\ | ||
- | From the Juropa home page: | ||
- | $WORK\\ | ||
- | File system for large temporary files with high I/O bandwidth demands | ||
- | (scratch file system). No backup of files residing here. Files not used | ||
- | for more than 28 days will be automatically deleted! | ||
- | |||
- | If you want to try the awimager try another build directly in the home | ||
- | directory / | ||
- | There are some weird problems with pyrap and this version uses a | ||
- | different compiler. The awimager seems to work but there are other | ||
- | problems which extend has not been analyzed yet. | ||
- | |||
- | |||
- | I hope these information are sufficient for some first tests and | ||
- | experiments.\\ | ||
- | Good luck and let me know of any problems and feel free to give some | ||
- | feedback. | ||
- | |||
- | |||
+ | ==== parset.py ==== | ||
+ | Changed the " | ||
+ | Should maybe be changed to the working directory?! | ||
- | on holidays for one week... after that more updates |