Category Archives: ROCKS

rocks-openmpi and gridengine in 5.4.3

it is well know that rocks-openmpi come with hpc roll in rocksclusters (5.4.3 current) did not compiled with-sge.e.g. /opt/openmpi/bin/ompi_info|grep gridengine return nothing (this bugs was fix by rocks’s developer the new rpm is here ) As an experiment, I download … Continue reading

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phpsysinfo in Rocks-5.4.3

I was able to get phpsysinfo going by the followings steps1) got http://www.applesauceman.com/ius/stable/Redhat/5/x86_64/2) download and install (need to remove all php-5.1(not sure all rpms  are required)http://www.applesauceman.com/ius/stable/Redhat/5/x86_64/epel-release-5-4.noarch.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-cli-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-common-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-devel-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-gd-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-mbstring-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-mysql-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-pdo-5.2.17-1.ius.el5.x86_64.rpmhttp://www.applesauceman.com/ius/stable/Redhat/5/x86_64/php52-xml-5.2.17-1.ius.el5.x86_64.rpm3)reboot the FE4)http://localhost/phpsysinfo/index.php?disp=dynamic  

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Changing Public DNS server for ROCKS 5.1

Every new version of Rockscluster has newer build in rocks cmd to make change of the information that store in the MySQL db. For older version one may need to direct interaction with the MySQL db: cluster and its tables … Continue reading

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Upgrade to Gromacs 4.5.3 or Gromacs 4.5.4 in rocks-5.4

bio-roll of rocks-5.4 come with gromacs-4.0.5, there are newer version of gromacs-4.5.3 and gromacs-4.5.4 how does one upgrade? The git site has newer bio roll that include gromacs 4.5.3, one can just download a snapshot http://git.rocksclusters.org/git/gitweb.cgi?p=core/bio/.git;a=tree by clicking the snapshot … Continue reading

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Rocks 5.4 FE as execd host

as of Rocks 5.4  adding FE(frontend) as execd host in SGE is very easy cd /opt/gridengine ./install_execd accept all default you should  adjust slots for the queue instance of the all.q@FE so it would not use all the CPU @FE … Continue reading

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useradd in 2nd HDD in r5.4

there is request that one want to spread some user on the 2nd HDD on rocks@FE the followings will work , there could be other way fdisk  /dev/sdb create partition 1 mkfs –t ext3 /dev/sdb1 mkdir /state/partition2; make sure it … Continue reading

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Rockscluster 4.3 in VirtualBox

Recently  in order to answer some question I need to install r4.3 in vbox env follow the standard method for r50-r54  the installation failed when one google the error message “ide: failed opcode was:0xef” one find out that for r4.3 … Continue reading

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setup login node in Rocks 5.4 with sge roll

there is new features in rocks 5.4.2 that one can configure login appliance it seems that it  is only work for sge roll and not yet with torque roll But one may need some extra steps to make the login … Continue reading

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How do you upgrade SGE in Rockscluster?

The r5.4 come with sge6.2u5 , the last version of opensource gridengine  that has some new features Enhanced Inspect Multiple AMI support for SDM EC2 Cloud Service Adapter Support for Machine Readable Table Output in SDM Slotwise Preemption Job to … Continue reading

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update python in rockscluster

download the python2.7 tar xfvz python2.7.tar.gz cd python2.7 run ./configure –prefix=/share/apps/python2.7 –with-threads –enable-shared make make install create python27.sh in /etc/profile.d if [ -d /share/apps/python2.7/bin ]; then export PATH=/share/apps/python2.7/bin:$PATH fi create python27.conf in /etc/ld.so.conf.d /share/apps/python2.7/lib one copy these files to all … Continue reading

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