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Q: GROMACS/gpgpu/README contains build and run instructions for the GPU version of GROMACS. It contains a reference to a file called gmx-gpgpu.tar.gz. This file is not in the supplied package?
A: This is a mistake from our side and the tar-file you were referring to is not actually needed. This file originally contained data to create the principal input file for the GPGPU run. But in the final moments we replaced this tarball with the actual principal input file gpu-bench.tpr.
We recommend to use the HOWTORUN-script in the root level of GROMACS directory and use of variable inputs=gpu-bench (and removing the 1 minute wonder part). Still, look also the Run Simulation section in the gpgpu/HOWTORUN -file.
Q: In the analysis of HELP we are observing that the process defined in the README file shows how to create an executable called su3_bench, but the job_scripts in directory L and XL expect an executable called HELP_30 and HELP_60 respectively. Are there any steps missing or should the executable created be renamed to what the job scripts are expecting?
A: HELP_30 & HELP_60 are symbolic links to the created su3_bench executable thus everything is in order.
Q: Page 31: "A.7.1 Summary of benchmark results The summary of benchmark results must include the following: "Elapsed time in seconds as reported in the file APPLICATION.time explained earlier in this Document"
--> We cannot see that the file APPLICATION.time is explained earlier in this Document?
A: Due to a typographical error the term/file "APPLICATION.time" has been thoroughly explained only in the file phase2_doc.txt (supplied together with the benchmark tarballs), section 3.2 "Timing files". It is paramount to electronically accompany these timing files together with the benchmark result files to CSC.
Q: We can't build AROME benchmark. It needs aeolus library, which included into package but does not completely build. It looks like we don't have all necessary files in package.
A: The benchmark version of AROME does not need the aeolus library and thus the source code under aeolus directory needs not to be built at all as it is never called in this configuration. Any unsatisfied external symbols referring to aeolus routines are automatically generated via gen_libdummy script through the make-system and placed into dummies.c. If you don't get any routines into the dummies.c (from MASTERODB try-build), then please check how to capture unsatisfied externals from your linker. There are numerous examples to browse through in the util/makeup/config.* -files. See also the util/makeup/gen_libdummy script and util/makeup/main.mk and define your UNDEF_GREPSTR in your config-file.