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"HDF5ERROR in aiori-HDF5.c (line 553): cannot create data set" error when benchmarking HDF5 in Blue Gene Q #9
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You are one up on me; IOR with HDF5 won't even compile for me on BG/Q. :) Did you have to make any modifications to get it to build?
Your screenshot says 1.8.8. Are you sure about that?
Sorry, I haven't used that version of IOR in at least two years. Off the top of my head, I know I changed the way IOR gets the host name to identify tasks per node. I think that made IOR's output a little more sane. I cannot remember if anything was more clearly broken than that. |
You are right, in my test I used 1.8.8 but I've just tested 1.8.10 and it returns the same error. About the compilation process, see if this helps: I didn't have to modify the source code, just past the parameters into the ./configure and make steps. HDF5 ZLIB Compiler In order to configure it for hdf5 building, I run: Then I just run make normally, and the make command would come up like this: I noticed now that I get two warning in the compilation process: This is the function where the execution dies, maybe its related to this issue? Then when running, I get the following output: HDF5-DIAG: Error detected in HDF5 (1.8.10) MPI-process 0: Began: Tue Jul 16 09:47:10 2013 Test 0 started: Tue Jul 16 09:47:10 2013 access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter ** error ** Hope this helps |
Yes, I would very much suspect that to be the case. The "(E)" denotes: "Error conditions exist that the compiler can correct, but the program might not produce the expected results." I am a bit surprised that the compiler doesn't halt, actually. I would dig into that error. |
Ok thank you. I will start looking into that. Let me know if you need help with the BGQ compilation. |
I too am surprised you could build this far. "aiori-HDF5.c", line 555.34: 1506-098 (E) Missing argument(s). means IOR is trying to use old-style HDF5 arguments. There is a backwards compatiblity option, though: add -DH5_USE_16_API to your cflags. Maybe IOR should just do that automatically. I shudder to think anyone is actually running HDF5-1.6.x, but even if they were that define would not affect them. |
I guess some day I'll set up my github life so I can "send a pull request. Until then, I blat patches into the issue tracker:
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Thanks, Rob! I added that change to master. |
It worked!! Thank you for you help Rob. |
Changed the semantics of -R to compare the data with the expected dat…
Hello
I'm having the following error when benchmarking the HDF5 method on a Blue Gene Q: "HDF5ERROR in aiori-HDF5.c (line 553): cannot create data set."
I'm using zlib/1.2.7 and hdf5/1.8.10, and compiling for the compute nodes (not front nodes).
The output is in this attachment below:
![ior-hdf5](https://camo.githubusercontent.com/c9f70698cf7b83bdc8ef470f92ac5ed66f6412cb56700023944dbf48a5245752/68747470733a2f2f662e636c6f75642e6769746875622e636f6d2f6173736574732f343939363739372f3739363633302f39613465386663362d656432622d313165322d383732662d3236663634626561343738622e706e67)
The file creation parameters are in this attachment below:
![backend-create-params](https://camo.githubusercontent.com/18358bca4a94933ea6aee3e6e626871645a1ff1a19f195349ca36d2a74d2e56b/68747470733a2f2f662e636c6f75642e6769746875622e636f6d2f6173736574732f343939363739372f3739363633322f61623865636339322d656432622d313165322d393531612d3137383263383738663963332e706e67)
I use the latest git master branch version (v. 3.0.1)
The MPIIO and POSIX tests work fine.
Thank you for your support.
PS: As per contract with IBM, I was told by my line manager that we have to use to the version 2.10.3 of IOR... is this version fully compatible with Blue Gene Q? Any known issues?
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