<div dir="ltr">Hi Adam,<br><br>I wanted to provide you with an update regarding my previous confusion regarding the "--mca" option. I have finally gained a clear understanding, and I can confirm that the "startdifx" command executed successfully without using the "--mca" option. I sincerely apologize for not thoroughly comprehending the implications of the "--mca" option, which caused the recurring issues with mpirun.<br><br>For testing purposes, I utilized the rdv70 dataset and followed the instructions outlined in the README file. Specifically, I used the command "diffDiFX.py reference_1.difx/DIFX_54656_074996.s0000.b0000 example_1.difx/DIFX_54656_074996.s0000.b0000 -i example_1.input" to compare my own computed results (example data) with the reference data. The final two lines of the displayed results were as follows:<br><br>"At the end, 1320 records disagreed on the header.<br>After 1848 records, the mean percentage absolute difference is 67.67053685, and the mean difference is 2.27732242 + 5.89398558 i."<br><br>Although I did not encounter any issues during the data processing, it appears that there are substantial differences in the comparison results. I am uncertain about the specific step that might have caused this problem.<br><br>Furthermore, when I generated the directory for the 1234 files using the "difx2mark4 -e 1234 example_1.difx" command, I encountered an issue when executing the command "fourfit -pt -c ../1234 191-2050" within the 1234 directory. The resulting error messages were as follows:<br><br>"fourfit: Invalid $block statement '$STATION A B BR-VLBA AXEL 2.0000 90.0 ......<br>fourfit: Failure in locate_blocks()<br>fourfit: Low-level parse of '/home/wude/difx/test_data/rdv70/1234/191-2050//4C39_25.2SN1CT' failed<br>fourfit: The above errors occurred while processing<br>fourfit: 191-2050//4C39_25.2SN1CT<br>fourfit: the top-level resolution is as follows: Error reading root for file 191-2050/, skipping."<br><br>However, when I conducted a test using the tc016a.pulsar dataset and ran the command "fourfit -pt -c ../1234 No0040," I successfully obtained the interference fringe image.<br><br>Thank you for your time and support.<br><br>Best regards,<br><br><div>De Wu</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Adam Deller <<a href="mailto:adeller@astro.swin.edu.au" target="_blank">adeller@astro.swin.edu.au</a>> 于2023年7月6日周四 12:19写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Sorry, I just saw that you had done this (and reported in your second email):<div><i><br></i></div><div><i>Subsequently, I proceeded to run the command "mpirun -np 8 -machinefile wude_1.machines mpifxcorr wude_1.input," and I was able to obtain the ".difx" files successfully.</i><br></div><div><br></div><div>So if you edit the startdifx file and find where mpirun is being invoked, and remove those --mca options, you should be fine.</div><div><br></div><div>Cheers,</div><div>Adam</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, 6 Jul 2023 at 14:16, Adam Deller <<a href="mailto:adeller@astro.swin.edu.au" target="_blank">adeller@astro.swin.edu.au</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Wu,<div><br></div><div>calcif2 is the delay-generating program that requires the calcserver to be running (which wasn't the case for you). Setting DIFX_CALC_PROGRAM=difxcalc determines which program which will be called by startdifx. But you were trying to run calcif2 itself from the command line, so naturally this won't work. If you run difxcalc wude_1.calc, it should work. And as you saw, if you run startdifx after setting DIFX_CALC_PROGRAM=difxcalc , that also works fine.</div><div><br></div><div>Once you have run difxcalc (or calcif2) the .im file will be generated. If you try to run difxcalc/calcif2 again once the .im file has been generated, it won't run unless you force it (since it sees that the .im file has been generated, so no need to re-generate it).</div><div><br></div><div>So your remaining problem now is that MPI seems to think that you don't have any available CPUs on your host. Once again (I think this is the third time I'm making this suggestion): please try running the mpirun command *without* the --mca options. I.e., </div><div><br></div><div>mpirun -np 4 --hostfile wude_1.machines runmpifxcorr.DiFX-2.6.2 wude_1.input<br></div><div><br></div><div>You may also have success by adding --oversubscribe to the mpirun command (although that is more of a band-aid getting around the fact that it seems that openmpi isn't seeing how many CPUs are available).</div><div><br></div><div>If you can figure out what mpirun option is causing the problem, you will then be able to modify startdifx to remove the offending option for you always.</div><div><br></div><div>Cheers,</div><div>Adam</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 4 Jul 2023 at 17:30, 深空探测 <<a href="mailto:wude7826580@gmail.com" target="_blank">wude7826580@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Subject: Issue with DiFX Testing - RPC Errors and CPU Allocation<br><br>Hi Adam,<br><div><br></div><div>I apologize for the delay in getting back to you. I've been conducting tests with DiFX lately, and I encountered a few issues that I would appreciate your insight on.<br><br>Initially, I faced problems running the `mpirun` command, but I managed to resolve them by reinstalling DiFX on a new CentOS7 system. Previously, I had installed `openmpi-1.6.5` in the `/usr/local` directory, but this time, I used the command `sudo yum install openmpi-devel` to install `openmpi`, and then I installed DiFX in the `/home/wude/difx/DIFXROOT` directory. Following this setup, the `mpirun` command started working correctly. I suspect that the previous installation in the system directory might have been causing the issues with `mpirun`.<br><br>However, I encountered a new problem when running the command `calcif2 wude_1.calc`. The output displayed the following error:<br><br>----------------------------------------------------------------------------------------<br>calcif2 processing file 1/1 = wude_1<br>localhost: RPC: Program not registered<br>Error: calcif2: RPC clnt_create fails for host: localhost<br>Error: Cannot initialize CalcParams<br>----------------------------------------------------------------------------------------<br><br>Previously, I resolved a similar error by running the command: `export DIFX_CALC_PROGRAM=difxcalc`. However, when I tried the same solution this time, it didn't resolve the issue.<br><br>Additionally, when running the command: `mpirun -np 4 --hostfile wude_1.machines --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 wude_1.input`, the output displayed the following message:<br><br>---------------------------------------------------------------------------------------------------------------<br>While computing bindings, we found no available CPUs on the following node:<br> Node: wude<br>Please check your allocation.<br>---------------------------------------------------------------------------------------------------------------<br><br>My hostname is "wude", and it seems like there are no available CPUs, but I can't determine the cause of this issue. Hence, I am reaching out to seek your guidance on this matter.<br><br>Thank you for your time and support.<br><br>Best regards,<br><br></div><div>De Wu</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Adam Deller <<a href="mailto:adeller@astro.swin.edu.au" target="_blank">adeller@astro.swin.edu.au</a>> 于2023年6月26日周一 07:36写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Have you tried removing the --mca options from the command? E.g., <div><br></div><div>mpirun -np 4 --hostfile /vlbi/aov070/aov070_1.machines runmpifxcorr.DiFX-2.6.2 /vlbi/aov070/aov070_1.input<br></div><div><br></div><div>I have a suspicion that either the seq or rmaps option is not playing nice, but it is easiest to just remove all the options and see if that makes any difference.</div><div><br></div><div>Cheers,</div><div>Adam</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 26 Jun 2023 at 01:58, 深空探测 <<a href="mailto:wude7826580@gmail.com" target="_blank">wude7826580@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Adam,<br><br>As you suggested, I removed the "| head" from the command, and I was able to run it successfully.<br><br>However, when executing the following command: "mpirun -np 4 --hostfile /vlbi/aov070/aov070_1.machines --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 /vlbi/aov070/aov070_1.input". The output displayed the following message:<br><br>--------------------------------------------------------------------------<br>mpirun noticed that the job aborted, but has no info as to the process<br>that caused that situation.<br>--------------------------------------------------------------------------<br><br>Additionally, when running the command "mpirun -np 4 -H localhost,localhost,localhost,localhost --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 /vlbi/aov070/aov070_1.input," and it resulted in the following error message:<br><br>--------------------------------------------------------------------------<br>There are no nodes allocated to this job.<br>--------------------------------------------------------------------------<br><br>It is quite puzzling that even when specifying only one localhost in the command, I still receive this output. I have been considering the possibility that this issue might be due to limitations in system resources, node access permissions, or node configuration within the CentOS7 virtual machine environment.<br><br>Thank you for your attention to this matter.<br><br>Best regards,<br><br><div>De Wu</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Adam Deller <<a href="mailto:adeller@astro.swin.edu.au" target="_blank">adeller@astro.swin.edu.au</a>> 于2023年6月22日周四 15:53写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi De Wu,<div><br></div><div>The "SIGPIPE detected on fd 13 - aborting" errors when running mpispeed are related to piping the output to head. Remove the "| head" and you should see it run normally.</div><div><br></div><div>For running mpifxcorr, the obvious difference between your invocation of mpispeed and mpifxcorr is the use of the various mca options. What happens if you add " --mca mpi_yield_when_idle 1 --mca rmaps seq" to your mpispeed launch (before or after the -H localhost,localhost)? If it doesn't work, then probably one or the other of those options is the problem, and you need to change startdifx to get rid of the offending option when running mpirun.</div><div><br></div><div>If running mpispeed still works when with those options, what about the following:</div><div>1. manually run mpirun -np 4 --hostfile /vlbi/aov070/aov070_1.machines --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 /vlbi/aov070/aov070_1.input, see what output comes out</div><div>2. manually run mpirun -np 4 -H localhost,localhost,localhost,localhost --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 /vlbi/aov070/aov070_1.input, see what output comes out</div><div><br></div><div>Cheers,</div><div>Adam</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 19 Jun 2023 at 18:02, 深空探测 via Difx-users <<a href="mailto:difx-users@listmgr.nrao.edu" target="_blank">difx-users@listmgr.nrao.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello,<div><br>I recently reinstalled OpenMPI-1.6.5 and successfully ran the example program provided within the OpenMPI package. By executing the command "mpiexec -n 6 ./hello_c," I obtained the following output:<br><br>```<br>wude@wude DiFX-2.6.2 examples> mpiexec -n 6 ./hello_c<br>Hello, world, I am 4 of 6<br>Hello, world, I am 2 of 6<br>Hello, world, I am 0 of 6<br>Hello, world, I am 1 of 6<br>Hello, world, I am 3 of 6<br>Hello, world, I am 5 of 6<br>```<br><br>The program executed without any issues, displaying the expected output. Each line represents a separate process, showing the process number and the total number of processes involved.<br><br>However, I encountered some difficulties when running the command "mpirun -H localhost,localhost mpispeed 1000 10s 1 | head." Although both nodes seem to run properly, there appear to be some errors in the output. Below is the output I received, with "wude" being my username:<br><br>```<br>wude@wude DiFX-2.6.2 ~> mpirun -H localhost,localhost mpispeed 1000 10s 1 | head<br>Processor = wude<br>Rank = 0/2<br>[0] Starting<br>Processor = wude<br>Rank = 1/2<br>[1] Starting<br>[1] Recvd 0 -> 0 : 2740.66 Mbps curr : 2740.66 Mbps mean<br>[1] Recvd 1 -> 0 : 60830.52 Mbps curr : 5245.02 Mbps mean<br>[1] Recvd 2 -> 0 : 69260.57 Mbps curr : 7580.50 Mbps mean<br>[1] Recvd 3 -> 0 : 68545.44 Mbps curr : 9747.65 Mbps mean<br>[wude:05649] mpirun: SIGPIPE detected on fd 13 - aborting<br>mpirun: killing job...<br><br>[wude:05649] mpirun: SIGPIPE detected on fd 13 - aborting<br>mpirun: killing job...<br>```<br><br>I'm unsure whether you experience the same "mpirun: SIGPIPE detected on fd 13 - aborting mpirun: killing job..." message when running this command on your computer.<br><br>Furthermore, when I ran the command "startdifx -v -f -n aov070.joblist," the .difx file was not generated. Could you please provide some guidance or suggestions to help me troubleshoot this issue?<br><br>Here is the output I received when running the command:<br><br>```<br>wude@wude DiFX-2.6.2 aov070> startdifx -v -f -n aov070.joblist<br>No errors with input file /vlbi/aov070/aov070_1.input<br><br>Executing: mpirun -np 4 --hostfile /vlbi/aov070/aov070_1.machines --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 /vlbi/aov070/aov070_1.input<br>--------------------------------------------------------------------------<br>mpirun noticed that the job aborted, but has no info as to the process<br>that caused that situation.<br>--------------------------------------------------------------------------<br>Elapsed time (s) = 82.2610619068<br>```<br><div>Best regards,<br><br></div><div>De Wu</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Adam Deller <<a href="mailto:adeller@astro.swin.edu.au" target="_blank">adeller@astro.swin.edu.au</a>> 于2023年5月25日周四 08:42写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi De Wu,<div><br></div><div>If I run </div><div><br></div><div>mpirun -H localhost,localhost mpispeed 1000 10s 1</div><div><br></div><div>it runs correctly as follows:</div><div><br></div><div>adeller@ar313-adeller trunk Downloads> mpirun -H localhost,localhost mpispeed 1000 10s 1 | head<br>Processor = <my host name><br>Rank = 0/2<br>[0] Starting<br>Processor =<my host name><br>Rank = 1/2<br>[1] Starting<br></div><div><br></div><div>It seems like in your case, MPI is looking at the two identical host names you've given and is deciding to only start one process, rather than two. What if you run </div><div><br></div><div>mpirun -n 2 -H wude,wude mpispeed 1000 10s 1</div><div><br></div><div>?</div><div><br></div><div>I think the issue is with your MPI installation / the parameters being passed to mpirun. Unfortunately as I've mentioned previously the behaviour of MPI with default parameters seems to change from implementation to implementation and version to version - you just need to track down what is needed to make sure it actually runs the number of processes you want on the nodes you want!</div><div><br></div><div>Cheers,<br>Adam</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 24 May 2023 at 18:30, 深空探测 via Difx-users <<a href="mailto:difx-users@listmgr.nrao.edu" target="_blank">difx-users@listmgr.nrao.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi All,<div><br></div><div>I am writing to seek assistance regarding an issue I encountered while working with MPI on a CentOS 7 virtual machine.<br></div><div><br>I have successfully installed openmpi-1.6.5 on the CentOS 7 virtual machine. However, when I attempted to execute the command "startdifx -f -n -v aov070.joblist," I received the following error message:<br><br>"Environment variable DIFX_CALC_PROGRAM was set, so<br>Using specified calc program: difxcalc<br><br>No errors with input file /vlbi/corr/aov070/aov070_1.input<br><br>Executing: mpirun -np 4 --hostfile /vlbi/corr/aov070/aov070_1.machines --mca mpi_yield_when_idle 1 --mca rmaps seq runmpifxcorr.DiFX-2.6.2 /vlbi/corr/aov070/aov070_1.input<br>--------------------------------------------------------------------------<br>mpirun noticed that the job aborted, but has no info as to the process that caused that situation.<br>--------------------------------------------------------------------------"<br><br>To further investigate the MPI functionality, I wrote a Python program “mpi_hello_world.py” as follows:</div><div><br>from mpi4py import MPI<br><br>comm = MPI.COMM_WORLD<br>rank = comm.Get_rank()<br>size = comm.Get_size()<br><br>print("Hello from rank", rank, "of", size)<br><br>When I executed the command "mpiexec -n 4 python mpi_hello_world.py," the output was as follows:<br><br>('Hello from rank', 0, 'of', 1)<br>('Hello from rank', 0, 'of', 1)<br>('Hello from rank', 0, 'of', 1)<br>('Hello from rank', 0, 'of', 1)<br><br>Additionally, I attempted to test the MPI functionality using the "mpispeed" command with the following execution command: "mpirun -H wude,wude mpispeed 1000 10s 1". “wude” is my hostname. However, I encountered the following error message:<br><br>"Processor = wude<br>Rank = 0/1<br>Sorry, must run with an even number of processes<br>This program should be invoked in a manner similar to:<br>mpirun -H host1,host2,...,hostN mpispeed [<numSends>|<timeSend>s] [<sendSizeMByte>]<br> where<br> numSends: number of blocks to send (e.g., 256), or<br> timeSend: duration in seconds to send (e.g., 100s)<br>--------------------------------------------------------------------------<br>mpirun noticed that the job aborted, but has no info as to the process that caused that situation.<br>--------------------------------------------------------------------------"<br><br>I am uncertain about the source of these issues and would greatly appreciate your guidance in resolving them. If you have any insights or suggestions regarding the aforementioned errors and how I can rectify them, please let me know.<br><br>Thank you for your time and assistance. <br><br>Best regards,<br><br></div><div>De Wu</div></div>
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</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px">!=============================================================!<br><div dir="ltr" style="font-size:12.8px">Prof. Adam Deller </div></div><div style="font-size:12.8px">Centre for Astrophysics & Supercomputing </div><div dir="ltr" style="font-size:12.8px">Swinburne University of Technology <br>John St, Hawthorn VIC 3122 Australia</div><div style="font-size:12.8px">phone: +61 3 9214 5307</div><div style="font-size:12.8px">fax: +61 3 9214 8797</div><div style="font-size:12.8px">!=============================================================!</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px">!=============================================================!<br><div dir="ltr" style="font-size:12.8px">Prof. Adam Deller </div></div><div style="font-size:12.8px">Centre for Astrophysics & Supercomputing </div><div dir="ltr" style="font-size:12.8px">Swinburne University of Technology <br>John St, Hawthorn VIC 3122 Australia</div><div style="font-size:12.8px">phone: +61 3 9214 5307</div><div style="font-size:12.8px">fax: +61 3 9214 8797</div><div style="font-size:12.8px">!=============================================================!</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px">!=============================================================!<br><div dir="ltr" style="font-size:12.8px">Prof. Adam Deller </div></div><div style="font-size:12.8px">Centre for Astrophysics & Supercomputing </div><div dir="ltr" style="font-size:12.8px">Swinburne University of Technology <br>John St, Hawthorn VIC 3122 Australia</div><div style="font-size:12.8px">phone: +61 3 9214 5307</div><div style="font-size:12.8px">fax: +61 3 9214 8797</div><div style="font-size:12.8px">!=============================================================!</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px"><div dir="ltr" style="font-size:12.8px">!=============================================================!<br><div dir="ltr" style="font-size:12.8px">Prof. Adam Deller </div></div><div style="font-size:12.8px">Centre for Astrophysics & Supercomputing </div><div dir="ltr" style="font-size:12.8px">Swinburne University of Technology <br>John St, Hawthorn VIC 3122 Australia</div><div style="font-size:12.8px">phone: +61 3 9214 5307</div><div style="font-size:12.8px">fax: +61 3 9214 8797</div><div style="font-size:12.8px">!=============================================================!</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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