====== How to use the MBB platform (Montpellier Bioinformatics Biodiversity computing cluster) ====== fc - 17.3.2014 This documentation summarizes information to help **AMAP agents** to connect with the ssh protocol on the MBB cluster and launch heavy computations. AMAP is part of the [[https://www.agropolis.fr/actualites/2011-labex-centre-mediterraneen-environnement-biodiversite-cemeb.php|Labex Cemeb]] and the AMAP members can access the Labex resources, including the [[https://mbb.univ-montp2.fr/MBB/index.php|MBB platform]]. For questions about the MBB cluster, please have a look to the online documentation (see links below), then ask first the two AMAP referents: Francois de Coligny or Yves Dumont, before finally contacting the MBB team: Rémy Dernat (system), Julien Veyssier (development) or Khalid Belkhir. ===== The MBB plaform online documentation ===== * [[https://mbb.univ-montp2.fr/MBB/index.php|Direct link to the platform]] * [[https://kimura.univ-montp2.fr/calcul/|Documentation page (fr)]] For all works using the services of the Montpellier Bioinformatics Biodiversity computing platform, please add this text in your publications: "[Replace_with_your_project_name] analyses largely benefited from the Montpellier Bioinformatics Biodiversity computing cluster platform." ===== How to create a SSH access login on the MBB cluster (AMAP members only) ===== All AMAP members can ask for a login on the MBB cluster from any computer located in the AMAP buildings in Montpellier (PS1, PS2). For AMAP members located elsewhere, a fixed ip address will be requested by the MBB team. __To get such a SSH login, please contact F. de Coligny__, we will do it together (according to the MBB system administrator request). **Reminder** MBB web site: [[https://mbb.univ-montp2.fr/MBB/index.php|click there]] > click on Login (top of the page) > Create an account > Tracking system * requester name: de Coligny * requester email: coligny@cirad.fr * choose 'Account creation on MBB cluster (SSH)' * priority 'High' * requester first name: Francois * team: 'AMAP', * project description and software to use, * then a title and message for the mail requesting the validation to the MBB administrators: * user name * user email (will receive the 'confirmation and further instructions' mail) * user preferred login proposal for the MBB administrator * answer the spam prevention questions * submit the request You will get a mail response with the instruction to login on the cluster. ssh coligny@162.38.181.181 You will have a home directory created. Once logged in, you can choose a new password with: passwd ===== How to copy files into your home directory ===== Once logged in, you can use the Linux commands to create directories in your home directory: [[https://kimura.univ-montp2.fr/calcul_isem/category/bash/|Linux commands]]. [coligny@cluster1 ~]$ mkdir data [coligny@cluster1 ~]$ cd data [coligny@cluster1 data]$ To **copy a file with scp** from your computer to the **data/** directory on the cluster; open a terminal on your own computer and type something like this (adapt for your own file): coligny@marvin-13:~/workspace/amapstudio/data/opf$ scp sunflower_100.opf coligny@162.38.181.181:data/ Password: sunflower_100.opf 100% 142KB 142.4KB/s 00:00 To **copy a data/ directory** from your computer to the cluster into test/: coligny@marvin-13:~/des-trucs$ scp -r data/ coligny@162.38.181.181:test Password: archimed1Export.ops 100% 378 0.4KB/s 00:00 mod_Rauh_14.opf 100% 31MB 10.3MB/s 00:03 mod_Koriba_7.opf 100% 3812KB 3.7MB/s 00:00 archimed1.config 100% 486 0.5KB/s 00:00 two-trees.ops 100% 386 0.4KB/s 00:00 A documentation about scp: [[https://cc.in2p3.fr/docenligne/134/fr|(french)]] ==== Example 1: how to install AMAPstudio through svn (modellers full local copy) on the cluster in your home directory ==== Typing the commands below will create a workspace/amapstudio/ directory and get a local copy of AMAPstudio in it by running an svn checkout (AMAPstudio modelers grant level requested). [coligny@cluster1 ~]$ pwd /home/fdcoligny [coligny@cluster1 ~]$ mkdir workspace [coligny@cluster1 ~]$ cd workspace/ [coligny@cluster1 workspace]$ mkdir amapstudio [coligny@cluster1 workspace]$ cd amapstudio/ [coligny@cluster1 amapstudio]$ [coligny@cluster1 amapstudio]$ svn co --username coligny https://amap-dev.cirad.fr/svn/jeeb/trunk (...) A trunk/etc/simeo.models A trunk/etc/editoGreenPin.opf A trunk/etc/simeo.extension.list A trunk/etc/editoRedPin.gwa A trunk/etc/xplo.models A trunk/Readme.txt U trunk Révision 4393 extraite. ==== Example 2: how to install AMAPstudio (end-user IzPack installer) on the cluster ==== 1. create an AMAPstudio installer and copy it to the cluster coligny@marvin-13:~/workspace/amapstudio$ sh ant installer coligny@marvin-13:~/workspace/amapstudio$ scp AMAPstudio-setup.jar coligny@162.38.181.181:test/installer-test 2. run the installer on the cluster with the GUI on your machine (delays will be experienced due to data transfer time) ssh -f -Y coligny@162.38.181.181 java -jar test/installer-test/AMAPstudio-setup.jar ===== How to launch a job on the cluster ===== A documentation for the [[https://www.rocksclusters.org/roll-documentation/sge/5.2/|Sun Grid Engine (SGE)]] : the distributed resource management software used to launch jobs on the MBB cluster. See this particular page: [[https://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html|Submitting batch jobs]] explains how the **qsub**, **qdel** and **qstat** commands can be used to manage batch jobs on the cluster. You may also read the 'Introduction to sge' man page : man sge_intro ==== Example 1: how to compile AMAPstudio on the cluster ==== Note: AMAPstudio must be **compiled with java 1.6**. The master node on the cluster contains java 1.7, the compute-nodes run java 1.6 (17 March 2014) -> the compilaton must be launched on the cluster nodes with qsub to match the good java 1.6. 1. Open a terminal, login to the cluster and change directory to be in the AMAPstudio installation directory (contains simeo.sh) ssh coligny@162.38.181.181 (...) cd workspace/amapstudio/trunk 2. Prepare **an sge script** to launch 'sh ant clean compile': cat > ant-clean-compile.sge #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash # date sh ant clean compile date 3. Run the sge script with **qsub**: [coligny@cluster1 trunk]$ qsub ant-clean-compile.sge Your job 166092 ("ant-clean-compile.sge") has been submitted 4. Check the cluster statistics [coligny@cluster1 trunk]$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- (...) 165554 0.55500 PhyML mbb r 03/10/2014 07:52:56 mbb.q@compute-0-15.local 1 165557 0.55500 PhyML mbb r 03/10/2014 11:21:29 mbb.q@compute-0-19.local 1 166069 0.55500 g32407_top igalaxy r 03/17/2014 10:54:46 mbb.q@compute-0-14.local 1 166091 0.55500 macse mbb r 03/17/2014 14:29:32 mbb.q@compute-0-5.local 1 166092 0.00000 ant-clean- coligny qw 03/17/2014 14:30:25 1 5. When the job is over, get the job output [coligny@cluster1 trunk]$ less ant-clean-compile.sge.o166092 Mon Mar 17 14:30:32 CET 2014 Buildfile: build.xml clean: [delete] Deleting directory /home/fdcoligny/workspace/amapstudio/trunk/bin revision: [echo] Jeeb revision 4375 [echo] os.name: Linux [echo] os.arch: amd64 compile: [mkdir] Created dir: /home/fdcoligny/workspace/amapstudio/trunk/bin [javac] Compiling 1872 source files to /home/fdcoligny/workspace/amapstudio/trunk/bin [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 2608 files to /home/fdcoligny/workspace/amapstudio/trunk/bin [copy] Copied 28 empty directories to 9 empty directories under /home/fdcoligny/workspace/amapstudio/trunk/bin BUILD SUCCESSFUL Total time: 24 seconds Mon Mar 17 14:30:56 CET 2014 The compilation was successful ==== Example 2: how to run an AMAPstudio script on the cluster ==== This example shows how to run the script **ScriptTristan2012** on the cluster. This script needs two parameters: an 'ops' file name and an 'archimed' config file. All the related files must be copied on the cluster before running the script. The syntax to launch the script on a simple machine (needs adaptations on the cluster, see below). sh simeo.sh -p script jeeb.simeo.module.simeoeditor.scripts.ScriptTristan2012 opsFileName archimed1ConfigFileName 1. Copy the parameter files on the cluster On the cluster, prepare directories to host the parameter files. [coligny@cluster1 trunk]$ mkdir tristan-files [coligny@cluster1 trunk]$ cd tristan-files/ [coligny@cluster1 tristan-files]$ mkdir opf From your machine, copy the needed files into these directories. coligny@marvin-13:~/des-trucs/data$ scp * coligny@162.38.181.181:workspace/amapstudio/trunk/tristan-files Password: archimed1.config 100% 486 0.5KB/s 00:00 opf: not a regular file two-trees.ops 100% 386 0.4KB/s 00:00 coligny@marvin-13:~/des-trucs/data$ scp opf/* coligny@162.38.181.181:workspace/amapstudio/trunk/tristan-files/opf Password: mod_Koriba_7.opf 100% 2321KB 2.3MB/s 00:00 mod_Rauh_14.opf 2. Prepare **a sge script** to launch the Script (in the amapstudio install dir) script-Tristan-2012.sge #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash # date sh simeo.sh -p script jeeb.simeo.module.simeoeditor.scripts.ScriptTristan2012 tristan-files/two-trees.ops tristan-files/archimed1.config date 3. Run the script [coligny@cluster1 trunk]$ qsub script-Tristan-2012.sge Your job 166129 ("script-Tristan-2012.sge") has been submitted [coligny@cluster1 tristan-files]$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- (...) 166129 0.00000 script-Tri coligny qw 03/17/2014 15:41:10 1 4. When the job is over, get the output [coligny@cluster1 trunk]$ less script-Tristan-2012.sge.o166129 Mon Mar 17 15:41:17 CET 2014 64 bits architecture - max memory: 4096 mega bytes Default locale is: en Simeo root directory: /home/fdcoligny/workspace/amapstudio/trunk Simeo 0.9, (c) 2006-2014 F. de Coligny et al. This program comes with ABSOLUTELY NO WARRANTY; This is free software, and you are welcome to redistribute it under certain conditions; See COPYING and COPYING.LESSER for details. Simeo 0.9-4375 with pilot capsis.script.Pilot: correct boot at 17 Mar 2014 15:41:19 CET Launching script jeeb.simeo.module.simeoeditor.scripts.ScriptTristan2012... ScriptTristan2012... opsFileName : tristan-files/two-trees.ops archimed1ConfigFileName: tristan-files/archimed1.config Loading scene... EditoInitialParameters buildInitScene ()... initXExtension: 50.0 initYExtension: 50.0 -> Creating a cache for scene +1 in *overwrite mode* (overwrite original files, no copies to automatic directories) EditoModel createScene () addingMockup: /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf Loading /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf... Loading /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf... Loading /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf done EditoModel createScene () addingMockup: /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Koriba_7.opf Loading /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Koriba_7.opf... Loading /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Koriba_7.opf... Loading /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Koriba_7.opf done Initialization completed Memorizer capsis.extension.memorizer.DefaultMemorizer was correctly set for project Project_edito.p Checking first mockup... Mockup id: 1 Mockup a_filePath_0: /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf Mockup a_filePath_1: /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf Mockup fileName_1: mod_Rauh_14.opf Mockup opf: /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf Mockup file: /home/fdcoligny/workspace/amapstudio/trunk/tristan-files/opf/mod_Rauh_14.opf Archimed1ExportScript starting... configFileName: tristan-files/archimed1.config #mockups : 2 Archimed1ExportConfigReader found 8 parameters in tristan-files/archimed1.config record: radiativeModel = TranslucentModel:0 record: yToNorthAngle_CW_deg = 45 record: latitude_deg = 45 record: clearness = 0.5 record: time1 = 2012/1/1 record: time2 = 2012/31/24 record: numberOfPixels = 25000 (...)