[FLASH-USERS] Sedov problem: HDF5 error

[杨云鹏]

I don't know much about it, but it seems that the system dynamic library loader does not know where libhdf5.so is.
(The compiler and the linker knows, but not the loader.)

That's not an error about FLASH. It's just one of the typical dynamic-library-missing errors:
error while loading shared libraries: lib***.so.***: cannot open shared object file: No such file or directory

I suggest you google linux command ldd, or linker option -R / -rpath, or environment variable LD_LIBRARY_PATH.
Hope that could help.

2019-04-03 17:45:32"张含天" <saphirezhang at gmail.com>写道：

Dear all,


I am new to FLASH and I want to try the first model Sedov explosion problem. But I am getting the following error.


My test environment is, attached is my Makefile.h
ubuntu 18.04

FLASH 4.6
gcc; gfortran 7.3.0
MPICH 3.3a2
hdf5 1.8.16 & 1.10.5 (tested separately)


Everything works well if I setup FLASH without IO, followed the manual.
$ ./setup Sedov -auto +noio 
$  cd object/

$ sudo make
$ sudo mpirun -np -1 ./flash4

And the calculation can start. The result is attached result_noIO.


However, when I try the following,
$ ./setup Sedov -auto
$  cd object/

$ sudo make
After '$ make', the Linking in Units and Libraries is SUCCESS. And I can find the 'flash4' file in the object/.

Then when I try '$ sudo mpirun -np -1 ./flash4', it returns an error (attached result_IO).
  ./flash4: error while loading shared libraries: libhdf5.so.10: cannot open shared object file: No such file or directory

However, the file 'libhdf5.so.10' can be found in the path '/usr/local/hdf5/lib', as written  in Makefile.h.


I know that there should be something wrong with the HDF5. But I can run the examples of HDF5 (under hdf5/share/hdf5_examples/c). And I tried different versions, the results were the same.


Can anyone give me some suggestions about this problem?


Kind regrads



Hantian Zhang

Research group PLASMANT

Department of Chemistry, University of Antwerp

Campus Drie Eiken, Universiteitsplein 1

BE-2610 Wilrijk-Antwerp, Belgium




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