Hi Tyler: Thanks for the documentation! Do you feel like adding that to our Wiki so that other users will be able to browse/add to it?
Mike, where do you suppose these kind of stuff should go? The Documentation Wiki or Trac Wiki...? We should probably decide soon to avoid confusion. Cheers, Bernard -----Original Message----- From: [EMAIL PROTECTED] on behalf of Tyler Cruickshank Sent: Mon 14/08/2006 15:30 To: oscar-users@lists.sourceforge.net Subject: Re: [Oscar-users] Oscar-users Digest, Vol 3, Issue 12 Filesystems/NFS: Thanks for the helpful discussion all. I set up NFS to mount the dir that I need. If I wasnt having other problems with the model I could report on how NFS is working out in my situation. Bernard, I will have a look at the article that you suggest. Resources like that are always helpful. Speaking of resources, I bought O'Reilly's High Performance Linux Clusters (2005) book this weekend. It has a significant section on OSCAR. In general, the book seems to provide basic overview information with some specifics. So far, it has been very helpful to me. I feel as though I have a better grasp on what a cluster really is (all the various configurations) and what OSCAR really is. Germain to this email thread are "overview" sections on NFS and PVFS. While I have not read the entire book, I can say that I wish I had read it earlier. MPICH2: I had a specific request for details on how I built MPICH2 using PGI compilers for the cluster so I have pasted my installation "notes" file at the bottom of my message (I attached a file but the message bounced). The notes file follows along with the MPICH2 installation guide and has my other random install notes included. So far I have tested it using the MPICH2 installation guide tests but have not actually tested it with my intended application. When I do that I will try and write up a clean clear "guide". Basically, I got compiler options thru communication with PGI. They have not released an official doc on it yet, but they sent what they use. So I built and compiled MPICH2 on my server node and then tar'd up the directory and used the C3 tool 'cpush' to move it over to the nodes. This was easy and worked quickly. On the nodes, I untar'd in the same location as on the server node (using ssh to work on the nodes). I then used the MPICH2 docs to start the daemon up on the server and nodes and followed the very detailed MPICH2 guide to complete and test the setup. More details are included in my attached notes file. I will still try to write up a better set of "how tos" once I have the whole thing (including my model) working. -ty #--------------------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------------------- MPICH2 Installation Notes. Command line input and resultant output is included in this file. #---------------------------------------------------- August 1, 2006 16:34 #---------------------------------------------------- Downloaded MPICH2 to: /temp/mpich2-1.0.4 Created installation directory: /opt/mpich2-pgi-1.0.4 Created build directory: /temp/build-mpich2 Used the PGI documentation in combination with the July 30, 2006 MPICH2 installation documentation to come up with the following command that executes the configure script: ------------------------------------------------- Step 5: ------------------------------------------------- [EMAIL PROTECTED] /temp/build-mpich2]$ env CFLAGS="-fast -fpic" CXXFLAGS="-fast -fpic" FFLAGS="-fast -fpic" \ F90FLAGS="-fast -fpic" LDFLAGS="-fast -fpic" OPTFLAGS="-fast -fpic" \ CC="pgcc" CXX="pgCC" F90="pgf90" FC="pgf77" \ CPP="pgCC -E" /temp/mpich2-1.0.4/configure \ -prefix=/opt/mpich2-pgi-1.0.4 |& tee configure-8-8-06-8:15.log Where \ indicates command line line continutation. **The above represents the latest from PGI for configuring MPICH2. See PGI email to Tyler. Step 6. Now make: ------------------------------------------------- [EMAIL PROTECTED] /temp/build-mpich2/lib]$ make | & tee make-8-8-06-08:25.log Step 7. Now make install: ------------------------------------------------- [EMAIL PROTECTED] /temp/build-mpich2]$ make install | & tee install-8-8-06-08:36.log To remove installation: ------------------------------------------------- /opt/mpich2-pgi-1.0.4/sbin/mpeuninstall may be used to remove the installation Step 8. Add to PATH: ------------------------------------------------- I did this in my .cshrc. Step 9. Set up MPD: ------------------------------------------------- [EMAIL PROTECTED] ~]$ cd /home/tcruicks [EMAIL PROTECTED] ~]$ touch .mpd.conf [EMAIL PROTECTED] ~]$ chmod 600 .mpd.conf [EMAIL PROTECTED] ~]$ vi .mpd.conf Where .mpd.conf contains a single line: secretword=secretsofoscar *Note, /home is mounted on the nodes so this file is automatically present on each node. Step 9b. See Step cpush below: --------------------------------------------- Step 10. Bring MPD Ring Up: ------------------------------------------------- [EMAIL PROTECTED] ~]$ mpd & [1] 8634 [EMAIL PROTECTED] ~]$ mpdtrace Redrock [EMAIL PROTECTED] ~]$ mpdallexit [1] + Done mpd Step 11. Test MPD Ring: ------------------------------------------------- [EMAIL PROTECTED] ~]$ mpd & [1] 8656 [EMAIL PROTECTED] ~]$ mpiexec -n 1 /bin/hostname Redrock [EMAIL PROTECTED] ~]$ mpdallexit [1] + Done mpd Step 12. Communicate with Nodes?: ------------------------------------------------- First, I created the file mpd.conf in my home directory. The file contains 2 lines: aqoscarnode1 aqoscarnode2 [EMAIL PROTECTED] ~]$ ssh aqoscarnode1 date Warning: Permanently added 'aqoscarnode1,10.0.0.10' (RSA) to the list of known hosts. Warning: No xauth data; using fake authentication data for X11 forwarding. Tue Aug 8 08:48:56 MDT 2006 [EMAIL PROTECTED] ~]$ ssh aqoscarnode2 date Warning: Permanently added 'aqoscarnode2,10.0.0.11' (RSA) to the list of known hosts. Warning: No xauth data; using fake authentication data for X11 forwarding. Tue Aug 8 08:51:26 MDT 2006 Step 13. Start daemons on nodes: ------------------------------------------------- [EMAIL PROTECTED] ~]$ mpdboot -n 1 -f mpd.hosts [C:[EMAIL PROTECTED]:~]>mpdtrace Redrock So, the nodes didnt show. Have to do work around. [C:[EMAIL PROTECTED]:~]>mpd & [C:[EMAIL PROTECTED]:~]>mpdtrace -l Redrock_43028 (10.0.0.2) Step cpush (C3): ------------------------------------------- ssh'ed into the nodes and tried to run the mpd command. Well, the nodes dont have the new mpich2 directory. I need to use cpush to sync up the nodes with the server. First, I tar'd the mphic2 directory and then used cp[ush to get them to the nodes: [EMAIL PROTECTED] /opt]$ cpush mpich2.tar -/opt building file list ... done mpich2.tar building file list ... done mpich2.tar sent 1815481 bytes received 40 bytes 1210347.33 bytes/sec total size is 7823360 speedup is 4.31 sent 1815481 bytes received 40 bytes 1210347.33 bytes/sec total size is 7823360 speedup is 4.31 [EMAIL PROTECTED] /opt]$ ssh aqoscarnode1 Now, Ill need to untar them over there (both nodes). [EMAIL PROTECTED] /opt]$ ssh aqoscarnode2 Last login: Mon Jul 10 11:33:52 2006 [EMAIL PROTECTED] ~]# cd /opt [EMAIL PROTECTED] opt]# ls c3-4 env-switcher lam-7.0.6 lam-switcher-modulefile-7.0.6 modules mpich-ch_p4-gcc-1.2.7 mpich2.tar pbs pvm3 [EMAIL PROTECTED] opt]# tar -xvf mpich2.tar -C /opt Done. [EMAIL PROTECTED] temp]# cpush build-mpich2.tar /temp building file list ... done build-mpich2.tar building file list ... done build-mpich2.tar sent 2805879 bytes received 40 bytes 1122367.60 bytes/sec total size is 15790080 speedup is 5.63 sent 2805879 bytes received 40 bytes 801691.14 bytes/sec total size is 15790080 speedup is 5.63 [EMAIL PROTECTED] temp]# tar -xvf build-mpich2.tar -C /temp [C:[EMAIL PROTECTED]:~]>mpdboot -n 1 -f mpd.hosts [C:[EMAIL PROTECTED]:~]>mpdtrace aqoscarnode1 [C:[EMAIL PROTECTED]:~]>mpdboot -n 1 -f mpd.hosts [C:[EMAIL PROTECTED]:~]>mpdtrace aqoscarnode2 Step 14. -------------------------------------------- [C:[EMAIL PROTECTED]:~]>mpdtrace Redrock aqoscarnode2 aqoscarnode1 [C:[EMAIL PROTECTED]:~]>mpdringtest time for 1 loops = 0.00134992599487 seconds Step 15. ------------------------------------------------- [C:[EMAIL PROTECTED]:~]>mpiexec -l -n 30 hostname 2: aqoscarnode1.aqoscardomain 5: aqoscarnode1.aqoscardomain 1: aqoscarnode2.aqoscardomain 3: Redrock 8: aqoscarnode1.aqoscardomain 6: Redrock 12: Redrock 11: aqoscarnode1.aqoscardomain 4: aqoscarnode2.aqoscardomain 9: Redrock 18: Redrock 24: Redrock 0: Redrock 29: aqoscarnode1.aqoscardomain 14: aqoscarnode1.aqoscardomain 17: aqoscarnode1.aqoscardomain 7: aqoscarnode2.aqoscardomain 15: Redrock 23: aqoscarnode1.aqoscardomain 26: aqoscarnode1.aqoscardomain 25: aqoscarnode2.aqoscardomain 20: aqoscarnode1.aqoscardomain 16: aqoscarnode2.aqoscardomain 10: aqoscarnode2.aqoscardomain 19: aqoscarnode2.aqoscardomain 27: Redrock 21: Redrock 22: aqoscarnode2.aqoscardomain 13: aqoscarnode2.aqoscardomain 28: aqoscarnode2.aqoscardomain Step 16. ------------------------------------------------- [C:[EMAIL PROTECTED]:~]>mpiexec -n 5 /temp/build-mpich2/examples/cpi /temp/build-mpich2/examples/cpi: error while loading shared libraries: libpgc.so: cannot open shared object file: No such file or directory /temp/build-mpich2/examples/cpi: error while loading shared libraries: libpgc.so: cannot open shared object file: No such file or directory /temp/build-mpich2/examples/cpi: error while loading shared libraries: libpgc.so: cannot open shared object file: No such file or directory I think we need the PGI portability package on all machines? Download from PGI for free. Installing that now. OK, installed the portability package (tar file on Redrock at /temp). I used cpush to move the file over and then untar'd and moved the 3 resultant directories to /usr/pgi (which I created). I then cd into /usr/pgi and did the following on both nodes: cp ./lib-linux86-g225/*so ./ Before trying again, I added the LD_LIBRARY_PATH to my .cshrc file. Now, try again: [C:[EMAIL PROTECTED]:~]>mpiexec -n 5 /temp/build-mpich2/examples/cpi Process 0 of 5 is on Redrock Process 2 of 5 is on aqoscarnode1.aqoscardomain Process 3 of 5 is on Redrock Process 1 of 5 is on aqoscarnode2.aqoscardomain Process 4 of 5 is on aqoscarnode2.aqoscardomain pi is approximately 3.1415926544231230, Error is 0.0000000008333298 wall clock time = 0.043239 It worked. ******The portability package needs to be on all the nodes.****** >>> <[EMAIL PROTECTED]> 8/11/2006 2:11 AM >>> Send Oscar-users mailing list submissions to oscar-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/oscar-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of Oscar-users digest..." Today's Topics: 1. MPICH2 Follow-Up (Tyler Cruickshank) 2. Re: MPICH2 Follow-Up (Steven Blackburn) 3. Re: MPICH2 Follow-Up (Michael Edwards) 4. Re: MPICH2 Follow-Up (Bernard Li) ---------------------------------------------------------------------- Message: 1 Date: Thu, 10 Aug 2006 14:36:35 -0600 From: "Tyler Cruickshank" <[EMAIL PROTECTED]> Subject: [Oscar-users] MPICH2 Follow-Up To: <oscar-users@lists.sourceforge.net> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Hello. I have 2 items: 1) I believe that I have successfully built, installed, and pushed MPICH2 using PGI compilers. Once I am sure that it is working Ill write it up and send it on. 2) I have a question that illustrates my depth of understanding of clusters (lack of depth). I am trying to run a model where the compute nodes need access to the same input/output dirs and executables (perhaps this is always the case?). Right now, when the nodes try to do a job, they cant access the executable that lives on the server. How do I set the nodes up so that they are able to access the server node directories? I can imagine using cpush in some way or fully mounting the file systems? Thanks for listening/reading. -Tyler -------------- next part -------------- An HTML attachment was scrubbed... URL: http://sourceforge.net/mailarchive/forum.php?forum=oscar-users/attachments/20060810/b27a3d11/attachment.html ------------------------------ Message: 2 Date: Thu, 10 Aug 2006 22:03:18 +0100 (BST) From: Steven Blackburn <[EMAIL PROTECTED]> Subject: Re: [Oscar-users] MPICH2 Follow-Up To: oscar-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=iso-8859-1 I am a novice with clusters.... but I was planning to solve the same problem as you in one of two ways: a) The home directories are automatically shared by Oscar, so a user could log on to the head node, ssh to a client node and see her directories (including any executables she has built there). I get the impression this is the model used if your cluster is used by lots of people (e.g. in a commercial setting). After all, a normal user can probably only write to their home directory and /tmp. b) Parallel file systems exist, such as PVFS, which could be used to distribute a volume across several nodes. I was considering installing PVFS on all four nodes of my 'toy' cluster. The way I was hoping to install this was going to end up with a file system each node could access locally but which would be spread across (and shared by) all nodes in the system. Because the Oscar PVFS package is not currently maintained, I went for using the shared home dirs. If I get a bit more comfortable with the cluster, I might give the package a go and see if I can fix whatever might be broken in it. Remember that with either option, the I/O would be across the network, so file access might be inefficient (i.e. reading the same file over and over). I was thinking of copying any such files to /tmp but, as you say, cpush might be useful here. Is there a programatic interface to cpush, or just exec()? But I am only a novice at this and could have got entirely the wrong idea... Steve. --- Tyler Cruickshank <[EMAIL PROTECTED]> wrote: > Hello. > > I have 2 items: > > 1) I believe that I have successfully built, > installed, and pushed > MPICH2 using PGI compilers. Once I am sure that it > is working Ill write > it up and send it on. > > 2) I have a question that illustrates my depth of > understanding of > clusters (lack of depth). I am trying to run a > model where the compute > nodes need access to the same input/output dirs and > executables (perhaps > this is always the case?). Right now, when the > nodes try to do a job, > they cant access the executable that lives on the > server. How do I set > the nodes up so that they are able to access the > server node > directories? I can imagine using cpush in some way > or fully mounting > the file systems? > > Thanks for listening/reading. > > -Tyler ------------------------------ Message: 3 Date: Thu, 10 Aug 2006 22:57:31 -0500 From: "Michael Edwards" <[EMAIL PROTECTED]> Subject: Re: [Oscar-users] MPICH2 Follow-Up To: oscar-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Many people, in my experience, either run off their NFS mounted home directories or they copy any needed files to some local directory (/tmp is popular). The first way is easy, but I have had occasional problems when the clocks on the nodes get out of sync, because then the files on a given node will not neccesarily get updated if the copy on one of the other nodes changes. This shouldn't be an issue since OSCAR uses ntp to keep the clocks in sync (the system that had this problem had ntp turned off for some reason), but I guess it depends a bit on how often you are hitting your files. NFS also isn't really designed for high bandwith stuff I don't think. Copying your files to the local drive is a nice solution if the files are not extremely large (what that means exactly depends a lot on your network). Then you get the file transfer overhead out of the way at the begining and you are always sure of what files you have, because you put them there yourself. This also avoids file locking problems, and write timing issues that can creep into code made by lazy mpi programers like me :) If you have very big data files, or very high I/O bandwith for some reason, it becomes a very difficult problem. Very large clusters are tricky too. On 8/10/06, Steven Blackburn <[EMAIL PROTECTED]> wrote: > I am a novice with clusters.... but I was planning to > solve the same problem as you in one of two ways: > > a) The home directories are automatically shared by > Oscar, so a user could log on to the head node, ssh to > a client node and see her directories (including any > executables she has built there). I get the impression > this is the model used if your cluster is used by lots > of people (e.g. in a commercial setting). After all, a > normal user can probably only write to their home > directory and /tmp. > > b) Parallel file systems exist, such as PVFS, which > could be used to distribute a volume across several > nodes. I was considering installing PVFS on all four > nodes of my 'toy' cluster. The way I was hoping to > install this was going to end up with a file system > each node could access locally but which would be > spread across (and shared by) all nodes in the system. > > Because the Oscar PVFS package is not currently > maintained, I went for using the shared home dirs. If > I get a bit more comfortable with the cluster, I might > give the package a go and see if I can fix whatever > might be broken in it. > > Remember that with either option, the I/O would be > across the network, so file access might be > inefficient (i.e. reading the same file over and > over). I was thinking of copying any such files to > /tmp but, as you say, cpush might be useful here. Is > there a programatic interface to cpush, or just > exec()? > > But I am only a novice at this and could have got > entirely the wrong idea... > > Steve. > > > --- Tyler Cruickshank <[EMAIL PROTECTED]> wrote: > > > Hello. > > > > I have 2 items: > > > > 1) I believe that I have successfully built, > > installed, and pushed > > MPICH2 using PGI compilers. Once I am sure that it > > is working Ill write > > it up and send it on. > > > > 2) I have a question that illustrates my depth of > > understanding of > > clusters (lack of depth). I am trying to run a > > model where the compute > > nodes need access to the same input/output dirs and > > executables (perhaps > > this is always the case?). Right now, when the > > nodes try to do a job, > > they cant access the executable that lives on the > > server. How do I set > > the nodes up so that they are able to access the > > server node > > directories? I can imagine using cpush in some way > > or fully mounting > > the file systems? > > > > Thanks for listening/reading. > > > > -Tyler > > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Oscar-users mailing list > Oscar-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/oscar-users > ------------------------------ Message: 4 Date: Fri, 11 Aug 2006 01:10:41 -0700 From: "Bernard Li" <[EMAIL PROTECTED]> Subject: Re: [Oscar-users] MPICH2 Follow-Up To: <oscar-users@lists.sourceforge.net> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi guys: I will add to this thread by pointing you all to this article available at ClusterMonkey: http://www.clustermonkey.net//content/view/142/32/ Cheers, Bernard ________________________________ From: [EMAIL PROTECTED] on behalf of Michael Edwards Sent: Thu 10/08/2006 20:57 To: oscar-users@lists.sourceforge.net Subject: Re: [Oscar-users] MPICH2 Follow-Up Many people, in my experience, either run off their NFS mounted home directories or they copy any needed files to some local directory (/tmp is popular). The first way is easy, but I have had occasional problems when the clocks on the nodes get out of sync, because then the files on a given node will not neccesarily get updated if the copy on one of the other nodes changes. This shouldn't be an issue since OSCAR uses ntp to keep the clocks in sync (the system that had this problem had ntp turned off for some reason), but I guess it depends a bit on how often you are hitting your files. NFS also isn't really designed for high bandwith stuff I don't think. Copying your files to the local drive is a nice solution if the files are not extremely large (what that means exactly depends a lot on your network). Then you get the file transfer overhead out of the way at the begining and you are always sure of what files you have, because you put them there yourself. This also avoids file locking problems, and write timing issues that can creep into code made by lazy mpi programers like me :) If you have very big data files, or very high I/O bandwith for some reason, it becomes a very difficult problem. Very large clusters are tricky too. On 8/10/06, Steven Blackburn <[EMAIL PROTECTED]> wrote: > I am a novice with clusters.... but I was planning to > solve the same problem as you in one of two ways: > > a) The home directories are automatically shared by > Oscar, so a user could log on to the head node, ssh to > a client node and see her directories (including any > executables she has built there). I get the impression > this is the model used if your cluster is used by lots > of people (e.g. in a commercial setting). After all, a > normal user can probably only write to their home > directory and /tmp. > > b) Parallel file systems exist, such as PVFS, which > could be used to distribute a volume across several > nodes. I was considering installing PVFS on all four > nodes of my 'toy' cluster. The way I was hoping to > install this was going to end up with a file system > each node could access locally but which would be > spread across (and shared by) all nodes in the system. > > Because the Oscar PVFS package is not currently > maintained, I went for using the shared home dirs. If > I get a bit more comfortable with the cluster, I might > give the package a go and see if I can fix whatever > might be broken in it. > > Remember that with either option, the I/O would be > across the network, so file access might be > inefficient (i.e. reading the same file over and > over). I was thinking of copying any such files to > /tmp but, as you say, cpush might be useful here. Is > there a programatic interface to cpush, or just > exec()? > > But I am only a novice at this and could have got > entirely the wrong idea... > > Steve. > > > --- Tyler Cruickshank <[EMAIL PROTECTED]> wrote: > > > Hello. > > > > I have 2 items: > > > > 1) I believe that I have successfully built, > > installed, and pushed > > MPICH2 using PGI compilers. Once I am sure that it > > is working Ill write > > it up and send it on. > > > > 2) I have a question that illustrates my depth of > > understanding of > > clusters (lack of depth). I am trying to run a > > model where the compute > > nodes need access to the same input/output dirs and > > executables (perhaps > > this is always the case?). Right now, when the > > nodes try to do a job, > > they cant access the executable that lives on the > > server. How do I set > > the nodes up so that they are able to access the > > server node > > directories? I can imagine using cpush in some way > > or fully mounting > > the file systems? > > > > Thanks for listening/reading. > > > > -Tyler > > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Oscar-users mailing list > Oscar-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/oscar-users > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Oscar-users mailing list Oscar-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/oscar-users -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8731 bytes Desc: not available Url : http://sourceforge.net/mailarchive/forum.php?forum=oscar-users/attachments/20060811/a1deb4ef/attachment.bin ------------------------------ ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ------------------------------ _______________________________________________ Oscar-users mailing list Oscar-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/oscar-users End of Oscar-users Digest, Vol 3, Issue 12 ******************************************
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