Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
On Sun, 27 Mar 2011, 23:13:49 BST, Chris Dagdigian wrote: > If anyone feels like testing these and giving feedback I'd appreciate > it. Have only run it on the systems where I built the code so there is a > chance that the binaries will complain about missing dependencies or > some other issue on more pristine Linux systems. I'm not convinced it's actually worth trying to support a single binary in the community for that sort of reason -- not that I want to stop anyone. Is anyone interested in doing native packaging for systems other than RedHat and Debian? (The major problem with source dpkg & rpm is the java build dependencies which aren't available, and possibly plpa on RedHat.) > The Son of Grid Engine herd issues are mainly because building of it is > commented out in the build.xml file It was commented out because I couldn't it to build, but now understand why. > The Son of Grid Engine GUI issues are (I think) caused by missing > logo.png files -- the build process bombs out complaining that it can't > find a .png file that is needed to build one of the visualization panes. I originally couldn't get far enough to spot that, due to the confusion I mentioned, but I wonder how it failed to get into the repo. It's in there now -- I pushed a heap of changes over the weekend, including a partial sync with the Univa repo, presumably just too late for you. I'll look at amending the build instructions as a result. -- Sent from a mobile; excuse the result. ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
On Sun, Mar 27, 2011 at 06:13:49PM -0400, Chris Dagdigian wrote: The Son of Grid Engine GUI issues are (I think) caused by missing logo.png files -- the build process bombs out complaining that it can't find a .png file that is needed to build one of the visualization panes. This implies the need for a new logo. Any takers? :) -- Jesse Becker NHGRI Linux support (Digicon Contractor) ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
I built Son-of-GridEngine and the Github Grid Engine over the weekend, I'll post a blog entry about it on Monday. Links to 32 and 64 bit Linux binaries for both versions are at this short link: http://biote.am/sge If anyone feels like testing these and giving feedback I'd appreciate it. Have only run it on the systems where I built the code so there is a chance that the binaries will complain about missing dependencies or some other issue on more pristine Linux systems. Still needs testing but I'm getting back into being comfortable with the build process. Next step is Mac OS X The Son of Grid Engine herd issues are mainly because building of it is commented out in the build.xml file The Son of Grid Engine GUI issues are (I think) caused by missing logo.png files -- the build process bombs out complaining that it can't find a .png file that is needed to build one of the visualization panes. I'm going to do some testing of those binaries this week and also work on OS X builds. The goal on our end (bioteam) is to have curtesy binaries that we don't mind sharing with others. -Chris Dave Love wrote: Chris Dagdigian writes: Everything built from source without too much hassle ... including the java stuff classes, the GUI installer and the hadoop herd classes. Never got the hadoop stuff to build before so this was a first I finally figured out the problems with herd and the GUI installer too, though I've only built my version with some non-fundamental build changes. One thing that was fooling me was confusion between the IzPack distribution and 3rdparty/IzPack, partly because the build requires to write to the installed IzPack distribution; I wonder if that's actually necessary. Can anyone say what the exact Java dependencies are? If not, I'll try to build in a minimal VM sometime to check (modulo versions). I had compiled the gridengine codebase against an older version of berkelydb (one that still supports RPC server) that I had built and stored at /opt/berkeley-db/lib/libdb-4.7.so For what it's worth, I made changes to use the system libraries (with an aimk flag), but I don't remember if there was much too it. I should try to do some more work on rpm building. ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
Chris Dagdigian writes: > Everything built from source without too much hassle > > ... including the java stuff classes, the GUI installer and the hadoop > herd classes. Never got the hadoop stuff to build before so this was a first I finally figured out the problems with herd and the GUI installer too, though I've only built my version with some non-fundamental build changes. One thing that was fooling me was confusion between the IzPack distribution and 3rdparty/IzPack, partly because the build requires to write to the installed IzPack distribution; I wonder if that's actually necessary. Can anyone say what the exact Java dependencies are? If not, I'll try to build in a minimal VM sometime to check (modulo versions). > I had compiled the gridengine codebase against an older version of > berkelydb (one that still supports RPC server) that I had built and > stored at /opt/berkeley-db/lib/libdb-4.7.so For what it's worth, I made changes to use the system libraries (with an aimk flag), but I don't remember if there was much too it. I should try to do some more work on rpm building. ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
Hi All, So I got confused when reading the particular JIRA entries regarding Berkeley DB and what we are doing with Postgres. We have not removed it from Grid Engine (so sorry about that). We will add postgres in the future though - not for 8.0.0 Please read Joachim's follow up email for more background/info. Regards, Bill. On 2011-03-24, at 6:12 PM, Bill Bryce wrote: > Hi Chris > > I think the guys removed the Berkeley db support or at the very least > deprecated it. We now support Postgres. > > Since I am not in the dev team I can't comment on the details, but tomorrow I > will ask them. > > Bill > > Sent from my iPad > > On 2011-03-24, at 6:06 PM, "Chris Dagdigian" wrote: > >> >> I just did a 'git clone' of the current source over at Github and was >> able to build (I think) 100% of the code. This is a 64 bit system >> running CentOS 5.5 >> >> Everything built from source without too much hassle >> >> ... including the java stuff classes, the GUI installer and the hadoop >> herd classes. Never got the hadoop stuff to build before so this was a first >> >> Looks like Univa is going to call this "Grid Engine 8.0.0 alpha" at >> least according to the GUI and client versions that show up. >> >> So far a test installation as gone fine except for one small problem ... >> >> I had compiled the gridengine codebase against an older version of >> berkelydb (one that still supports RPC server) that I had built and >> stored at /opt/berkeley-db/lib/libdb-4.7.so >> >> >> The problem is that when I packege up my build and go to install Grid >> Engine, the install fails because when it tries to set up the inital >> berkeley spooling database the local SGE lib "libspoolb.so" complains >> about not being able to find "libdb-4.7.so" >> >> Easy fix on my test system via ld.so.conf or whatever but it makes me >> think that I've built something wrong ... I thought I was doing a static >> build where all the external libraries would come along for the ride ... >> >> Any aimk or aimk.site people have any tips for making sure the proper >> BDB libraries/objects accompany the courtesy binaries? >> >> dag >> >> >> ___ >> users mailing list >> users@gridengine.org >> https://gridengine.org/mailman/listinfo/users > > > - > > > Notice from Univa Postmaster: > > > This email message is for the sole use of the intended recipient(s) and may > contain confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited. If you are not the intended > recipient, please contact the sender by reply email and destroy all copies of > the original message. This message has been content scanned by the Univa Mail > system. > > > > - > > > ___ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users - Notice from Univa Postmaster: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. This message has been content scanned by the Univa Mail system. - ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
Hi Chris, we will be shipping Berkeley DB 4.4.20 with the 8.0.0 - to be compatible with 6.2u5 systems. We dropped support for the Berkeley DB RPC server (berkeley_db_svc) though. It is no longer supported in current versions of Berkeley DB (IIRC starting with 4.8). Regarding your issue with installation not finding the libdb.so: In the Berkeley DB binaries we ship with Grid Engine we set the runpath to ../../lib/ to make our binaries find the libdb.so without setting the LD_LIBRARY_PATH. There are 2 possible fixes for that: 1. When installing the binaries, call distinst with the option -shlibpath. With this option set, the installation will add $SGE_ROOT/lib/ to the LD_LIBRARY_PATH, and add code setting LD_LIBRARY_PATH to the settings.[c]sh files as well. 2. Build Berkeley DB in such a way that it contains the run path. Requires patching a file (dist/ltmain.sh) in the BDB code, and setting 2 environment variables during the BDB build: export LD_RUN_PATH='$ORIGIN/../../lib/lx-amd64' export ORIGIN='$ORIGIN' The patch (for bdb 4.4.20) is: 1318c1318,1324 <*) rpath="$rpath $arg" ;; --- > *) >if [ "$LD_RUN_PATH" = "" ]; then > rpath="$rpath $arg" >else > rpath="$rpath $LD_RUN_PATH" >fi >;; Joachim Chris Dagdigian wrote: I just did a 'git clone' of the current source over at Github and was able to build (I think) 100% of the code. This is a 64 bit system running CentOS 5.5 Everything built from source without too much hassle ... including the java stuff classes, the GUI installer and the hadoop herd classes. Never got the hadoop stuff to build before so this was a first Looks like Univa is going to call this "Grid Engine 8.0.0 alpha" at least according to the GUI and client versions that show up. So far a test installation as gone fine except for one small problem ... I had compiled the gridengine codebase against an older version of berkelydb (one that still supports RPC server) that I had built and stored at /opt/berkeley-db/lib/libdb-4.7.so The problem is that when I packege up my build and go to install Grid Engine, the install fails because when it tries to set up the inital berkeley spooling database the local SGE lib "libspoolb.so" complains about not being able to find "libdb-4.7.so" Easy fix on my test system via ld.so.conf or whatever but it makes me think that I've built something wrong ... I thought I was doing a static build where all the external libraries would come along for the ride ... Any aimk or aimk.site people have any tips for making sure the proper BDB libraries/objects accompany the courtesy binaries? dag ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users - Notice from Univa Postmaster: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. This message has been content scanned by the Univa Mail system. - ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
Hi Chris I think the guys removed the Berkeley db support or at the very least deprecated it. We now support Postgres. Since I am not in the dev team I can't comment on the details, but tomorrow I will ask them. Bill Sent from my iPad On 2011-03-24, at 6:06 PM, "Chris Dagdigian" wrote: > > I just did a 'git clone' of the current source over at Github and was > able to build (I think) 100% of the code. This is a 64 bit system > running CentOS 5.5 > > Everything built from source without too much hassle > > ... including the java stuff classes, the GUI installer and the hadoop > herd classes. Never got the hadoop stuff to build before so this was a first > > Looks like Univa is going to call this "Grid Engine 8.0.0 alpha" at > least according to the GUI and client versions that show up. > > So far a test installation as gone fine except for one small problem ... > > I had compiled the gridengine codebase against an older version of > berkelydb (one that still supports RPC server) that I had built and > stored at /opt/berkeley-db/lib/libdb-4.7.so > > > The problem is that when I packege up my build and go to install Grid > Engine, the install fails because when it tries to set up the inital > berkeley spooling database the local SGE lib "libspoolb.so" complains > about not being able to find "libdb-4.7.so" > > Easy fix on my test system via ld.so.conf or whatever but it makes me > think that I've built something wrong ... I thought I was doing a static > build where all the external libraries would come along for the ride ... > > Any aimk or aimk.site people have any tips for making sure the proper > BDB libraries/objects accompany the courtesy binaries? > > dag > > > ___ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users - Notice from Univa Postmaster: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. This message has been content scanned by the Univa Mail system. - ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] [gridengine dev] building on centos 5.5 64 bit?
I just did a 'git clone' of the current source over at Github and was able to build (I think) 100% of the code. This is a 64 bit system running CentOS 5.5 Everything built from source without too much hassle ... including the java stuff classes, the GUI installer and the hadoop herd classes. Never got the hadoop stuff to build before so this was a first Looks like Univa is going to call this "Grid Engine 8.0.0 alpha" at least according to the GUI and client versions that show up. So far a test installation as gone fine except for one small problem ... I had compiled the gridengine codebase against an older version of berkelydb (one that still supports RPC server) that I had built and stored at /opt/berkeley-db/lib/libdb-4.7.so The problem is that when I packege up my build and go to install Grid Engine, the install fails because when it tries to set up the inital berkeley spooling database the local SGE lib "libspoolb.so" complains about not being able to find "libdb-4.7.so" Easy fix on my test system via ld.so.conf or whatever but it makes me think that I've built something wrong ... I thought I was doing a static build where all the external libraries would come along for the ride ... Any aimk or aimk.site people have any tips for making sure the proper BDB libraries/objects accompany the courtesy binaries? dag ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
