Compile HDF5 for TOMOATT on NSCC

[JingChen-Thu]

Possibly due to the upgrade of NSCC system, I encountered some problem when compiling local HDF5 using this instruction: "https://tomoatt.com/docs/GetStarted/Use_on_HPCs"

After make -j16, an error occurred:

/usr/bin/ld: cannot find -lpmi2
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1002: libhdf5_cpp.la] Error 1
make[2]: Leaving directory '/home/users/ntu/jingchen/tomoatt/TomoATT/external_libs/hdf5-1.13.3/c++/src'
make[1]: *** [Makefile:895: all-recursive] Error 1
make[1]: Leaving directory '/home/users/ntu/jingchen/tomoatt/TomoATT/external_libs/hdf5-1.13.3/c++'
make: *** [Makefile:733: all-recursive] Error 1

It seems that "libpmi2.so" is not found. However, this file really exists, e.g., in "/opt/cray/pe/lib64".
Using
"export LD_LIBRARY_PATH=/opt/cray/pe/lib64:$LD_LIBRARY_PATH"
to include the path does not work. However, this command
"LIBRARY_PATH=/opt/cray/pe/lib64:$LIBRARY_PATH"
works. I do not really know the reason. But finally I succeeded. Just for your reference if you meet the same problem when compiling TomoATT on NSCC.

By the way, the module "openmpi/4.1.5-gcc11" is not available on NSCC since 2025. Please use "openmpi/4.1.6-gcc11" instead.

[JingChen-Thu]

Answered above.

[xumi1993]

Currently, TomoATT is no longer dependent on SIMD. Thus, try to compile it using Cray instead of GCC.

[mnagaso]

Hi Mijian,

Please let me precise it here.
TomoATT does not require SIMD from initial by changing an option defined in CMakeFiles.