Using large voxel numbers in Dosxyznrc

[Abdullah-Abuhaimed]

Dear all,

I am running simulations in Dosxyznrc using an obese full body phantom that has a large number of voxels (x=350, y=410, and z=652). When I change (IMAX,JMAX, and KMAX) in dosxyznrc_user_macros.mortran to these values, I get the error shown below. I have managed to run simulations with smaller phantoms with no issue, but not for large phantoms. It would be greatly appreciated if anyone could assist me in overcoming this issue.

Fortran compiling dosxyznrc_linux.F using flags ' -fPIC -O2 -mtune=native' and extra objects/libs '/project/k1508/EGSnrc/HEN_HOUSE/lib/linux/egs_c_utils.o /project/k1508/EGSnrc/HEN_HOUSE/lib/linux/read_write_pardose.o /project/k1508/EGSnrc/HEN_HOUSE/lib/linux/load_beamlib.o  /project/k1508/EGSnrc/HEN_HOUSE/lib/linux/load_vculib.o  -ldl -L/project/k1508/EGSnrc/HEN_HOUSE/egs++/dso/linux -Wl,-rpath,/project/k1508/EGSnrc/HEN_HOUSE/egs++/dso/linux -liaea_phsp'
/usr/bin/ld: failed to convert GOTPCREL relocation; relink with --no-relax
/usr/bin/sha1sum: /project/k1508/EGSnrc/egs_home/bin/linux/dosxyznrc: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/project/k1508/EGSnrc/HEN_HOUSE/makefiles/standard_makefile:90: /project/k1508/EGSnrc/egs_home/bin/linux/dosxyznrc] Error 1

[rtownson]

Try changing the compiler flags in the Makefile to allow for large arrays:
EGS_EXTRA_LIBS = $(FLIBS) $(BEAMLIB_EXTRA_LIBS) -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -mcmodel=large

This is a common question, there's more discussion here: https://www.reddit.com/r/EGSnrc/comments/jkcv4e/increase_the_maximun_number_of_voxels_in_xyz/

[crcrewso]

I'm wondering, with GCC is it time we add this to the default flags?

-mcmodel=medium
Generate code for the medium model: the program is linked in the lower 2 GB of the address space. Small symbols are also placed there. Symbols with sizes larger than -mlarge-data-threshold are put into large data or BSS sections and can be located above 2GB. Programs can be statically or dynamically linked.
-mcmodel=large
Generate code for the large model. This model makes no assumptions about addresses and sizes of sections.
Link

[Abdullah-Abuhaimed]

Thank you Reid for your response,

I have tried to add the options (all together or individually), but I got the error shown below. I modified both the Makefile in HEN_HOUSE/ and-or egs_home/, but sill no luck. Any idea?

Fortran compiling dosxyznrc_linux.F using flags ' -fPIC -O2 -mtune=native' and extra objects/libs '/project/k1508/EGSnrc/HEN_HOUSE/lib/linux/egs_c_utils.o /project/k1508/EGSnrc/HEN_HOUSE/lib/linux/read_write_pardose.o /project/k1508/EGSnrc/HEN_HOUSE/lib/linux/load_beamlib.o  /project/k1508/EGSnrc/HEN_HOUSE/lib/linux/load_vculib.o  -ldl -L/project/k1508/EGSnrc/HEN_HOUSE/egs++/dso/linux -Wl,-rpath,/project/k1508/EGSnrc/HEN_HOUSE/egs++/dso/linux -liaea_phsp -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -mcmodel=large'
/usr/bin/ld: failed to convert GOTPCREL relocation; relink with --no-relax
/usr/bin/sha1sum: /project/k1508/EGSnrc/egs_home/bin/linux/dosxyznrc: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/project/k1508/EGSnrc/HEN_HOUSE/makefiles/standard_makefile:90: /project/k1508/EGSnrc/egs_home/bin/linux/dosxyznrc] Error 1 

[rtownson]

You may need to re-run the installer (or HEN_HOUSE/scripts/configure if you're on linux) and add the flags for the fortran compilation there. This was discussed in the link I shared so maybe that was the extra step they took that worked. Also make sure you have enough RAM - that array size is nearly 1GB and it needs to be able to allocate several of them at once.

@crcrewso you're probably right, we should at least add -mcmodel=medium and see if that covers it.

[crcrewso]

Done, see #725

[Abdullah-Abuhaimed]

Thank you @rtownson for your support. I have managed to get the simulation worked by re-running the installer and adding the suggested options in the compiler flags, not only for fortran, but also for the other compilers.

[ftessier]

The -mcmodel=medium option has been added to the default compiler flags in the configure script and configuration gui. See #725.