[FLASH-USERS] Problem in LaserSlab simulation

[Marissa Adams]

Hi Zhang,

Check to make sure that the version of HDF5 you're using is parallelized. You can see more about using parallel HDF5 if you cmd+F search "parallel HDF5" in the user manual (http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug_4p5.pdf). In order to use the laser energy deposition in FLASH, this is required.

That version of HDF5 should be pretty good (1.8.17). You can check to see if it is parallel but open, or checking to see if the value is "TRUE" or "YES" or something like that via

grep "Parallel HDF5" /path/to/hdf5/lib/libhdf5.settings

Effectively you want to make sure that in that file, the version of HDF5 you've built, or the system has built is parallelized. If it isn't, I suppose you could make your own version in your home directory given your user permissions, or just ask your system administrator to build it for you.

I recommend reading section 17.4.10.4 LaserIO Runtime Parameters and Usage in the user manual for more information.

Hopefully, this alleviates the problem. If not, make sure your path to the same library is correct in your Makefile.h. For instance, sometimes people make the mistake of leaving /lib on the end.

Good luck!

Best,
Marissa Adams

---
Marissa Adams
PhD Student
Website: http://www.pas.rochester.edu/~madams<http://www.pas.rochester.edu/~madams/>
University of Rochester
Department of Physics & Astronomy
371 Bausch & Lomb Hall


On Wed, Oct 10, 2018 at 9:17 AM zdy0903 <zdy0903 at stu.xjtu.edu.cn<mailto:zdy0903 at stu.xjtu.edu.cn>> wrote:

Hello!

 I got some problems when I run the LaserSlab simulation in Flash4.4 with HDF5-1.8.17. It is fine when I set up. And after I execute make. It meet some errors just like



io_h5file_interface.o: In function `io_h5init_file_':
/home/zdy/Desktop/FLASH4.4/object/io_h5file_interface.c:165: undefined reference to `H5Pset_fapl_mpio'
io_h5file_interface.o: In function `io_h5open_file_for_read_':
/home/zdy/Desktop/FLASH4.4/object/io_h5file_interface.c:273: undefined reference to `H5Pset_fapl_mpio'
io_h5read_unknowns.o: In function `io_h5read_unknowns_':
/home/zdy/Desktop/FLASH4.4/object/io_h5read_unknowns.c:53: undefined reference to `H5Pset_dxpl_mpio'
io_h5write_unknowns.o: In function `io_h5write_unknowns_':
/home/zdy/Desktop/FLASH4.4/object/io_h5write_unknowns.c:156: undefined reference to `H5Pset_dxpl_mpio'
io_h5write_unknowns_sp.o: In function `io_h5write_unknowns_sp_':
/home/zdy/Desktop/FLASH4.4/object/io_h5write_unknowns_sp.c:237: undefined reference to `H5Pset_dxpl_mpio'
collect2: error: ld returned 1 exit status
Makefile:353: recipe for target 'flash4' failed
make: *** [flash4] Error 1


Is there anyone knows what it is about? Thanks a lot!


Zhang

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