May 2016 - Darshan-users - mailman3.cels.anl.gov

Re: [Darshan-users] compiling statically with intel toolchain
by Phil Carns 27 May '16

27 May '16

Great! We opened up a gitlab issue to see if we can add a graceful safety check for that case. thanks, -Phil On 05/24/2016 05:30 PM, Salmon, Rene wrote: > Success at last. Thank you all for the help. Again the info you provided gave me enough hints. > For whatever reason the version of gnuplot on my system did not know what to do with the ï¿½-eï¿½ flag. > All I did was upgrade gnuplot and now I have a nice PDF with graphs. > > This is good enough for me for now. I will run a few test and see what I can learn from the tool. > > Thanks again > Rene > > > > > On 5/24/16, 10:28 AM, "Phil Carns" <carns(a)mcs.anl.gov> wrote: > >> Gnuplot 4.2 should be Ok. I just confirmed that 4.2 patchlevel 6 works >> with darshan-job-summary.pl on one of our systems. >> >> You could try the following to check what happens to gnuplot when it >> tries to generate the first plot: >> >> - add --verbose to the darshan-job-summary.pl command line >> - look for "verbose: /tmp/1FMc4r0alx" (or something similar) in the >> first line of output >> - cd to that directory >> - run the gnuplot command manually: >> >> gnuplot -e "data_file='mpiio-access-hist.dat'; graph_title='MPI-IO >> Access Sizes {/Times-Bold=32 \263}'; >> output_file='mpiio-access-hist.eps'" access-hist-eps.gplt >> >> In theory it should run cleanly and create a mpiio-access-hist.eps >> output file. >> >> Thanks for your patience getting this stuff working, by the way. I'm not >> sure what can be done about the Intel MPI Fortran wrapper problem on our >> end, but if there is a gnuplot issue we should be able to work around it >> or at least gracefully detect the problem. >> >> thanks, >> -Phil >> >> On 05/24/2016 10:37 AM, Salmon, Rene wrote: >>> Hi, >>> >>> hpcbuild02(salmr0)1060:gnuplot -V >>> gnuplot 4.2 patchlevel 3 >>> >>> >>> >>> Thanks >>> Rene >>> >>> >>> >>> On 5/24/16, 9:35 AM, "Phil Carns" <carns(a)mcs.anl.gov> wrote: >>> >>>> Hi Rene, >>>> >>>> What version of gnuplot do you have ("gnuplot -V")? >>>> >>>> Darshan is supposed to have a safety check for the presence of gnuplot >>>> and it's version, but the "-e" thing is part of the gnuplot command >>>> line. Maybe something has gone wrong there. >>>> >>>> thanks, >>>> -Phil >>>> >>>> On 05/24/2016 10:21 AM, Salmon, Rene wrote: >>>>> All, >>>>> >>>>> Thank you very much for all the help and info. I now have a working binary that does generate a darshan log file. Your hints where very helpful. What I ended up doing was writing an mpi_init and mpi_finalize wrapper in C that my fortran code calls and that seems to work and now I can generate a darshan log file. >>>>> >>>>> I basically just call my_finalize() from my fortran code and that is just this: >>>>> >>>>> #include "mpi.h" >>>>> int my_finalize_(void) >>>>> { >>>>> int ier; >>>>> ier = MPI_Finalize(); >>>>> return(ier); >>>>> } >>>>> >>>>> >>>>> Now I just want to analyze the results so I run the darshan-job-summary.pl but I am getting these errors. Any ideas what they mean? >>>>> >>>>> hpcbuild02(salmr0)1054:darshan-job-summary.pl ./salmr0_ddswriter_id40315_5-24-32872-5756027388706526063_1.darshan >>>>> Slowest unique file time: 0.004726 >>>>> Slowest shared file time: 0.011293 >>>>> Total bytes read and written by app (may be incorrect): 51934 >>>>> Total absolute I/O time: 0.016019 >>>>> **NOTE: above shared and unique file times calculated using MPI-IO timers if MPI-IO interface used on a given file, POSIX timers otherwise. >>>>> Cannot open load file '-e' >>>>> line 0: util.c: No such file or directory >>>>> >>>>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>>>> !!! Error: 'posix-access-hist.eps' does not exist! >>>>> Cannot open load file '-e' >>>>> line 0: util.c: No such file or directory >>>>> >>>>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>>>> !!! Error: 'file-access-read.eps' does not exist! >>>>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>>>> !!! Error: 'file-access-write.eps' does not exist! >>>>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>>>> !!! Error: 'file-access-shared.eps' does not exist! >>>>> LaTeX generation (phase1) failed [17920], aborting summary creation. >>>>> error log: >>>>> Overfull \hbox (18.76118pt too wide) in paragraph at lines 52--52 >>>>> [][] >>>>> <time-summary.pdf, id=1, 289.08pt x 252.945pt> <use time-summary.pdf> >>>>> <op-counts.pdf, id=2, 289.08pt x 252.945pt> <use op-counts.pdf> >>>>> >>>>> LaTeX Warning: File `posix-access-hist.pdf' not found on input line 68. >>>>> >>>>> >>>>> !pdfTeX error: pdflatex (file posix-access-hist.pdf): cannot find image file >>>>> ==> Fatal error occurred, no output PDF file produced! >>>>> >>>>> >>>>> Thanks >>>>> Rene >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 5/23/16, 5:21 PM, "Harms, Kevin" <harms(a)alcf.anl.gov> wrote: >>>>> >>>>>> Rene, >>>>>> >>>>>> Your code is making the mpi_init and mpi_finalize call from Fortran correct? You are still hitting the same issue as you noted before which is that the Darshan doesnï¿½t intercept those calls with the Intel MPI implementation. You could specifically add the darshan calls to your Fortran code manually. It isnï¿½t pretty but it should work. This will initialize the library and then it should capture all the calls from your I/O code since that is all in C. >>>>>> >>>>>> call mpi_init() >>>>>> call darshan_core_initialize(%VAL(0), %VAL(0)); >>>>>> ï¿½ >>>>>> call darshan_core_shutdown(); >>>>>> call mpi_finalize() >>>>>> >>>>>> depending on the function names, you may need to add an underscore to the end of the names. >>>>>> >>>>>> kevin >>>>>> >>>>>>> Hi Phil, >>>>>>> >>>>>>> Thanks for the info that was helpful. I did manage to link in darshan and MPI statically I had to put in the ï¿½lib.aï¿½ files by hand as the ï¿½darshan-config ï¿½pre/postï¿½ scripts where still trying to link in darshan dynamically. >>>>>>> Here is the link line I used that seem to generate a binary. >>>>>>> >>>>>>> >>>>>>> mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o /hpcdata/salmr0/mspain/usp2hdf5/dds/bin/Linux/3.0/x86_64/ddswriter.revUnversioned /hpc/tstapps/intel/x86_64/ics-2016.update.1/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.a -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a -lz -Wl,@/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/share/ld-opts/darshan-base-ld-opts svn_version.o PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib -Wl,--start-group /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan-stubs.a -Wl,--end-group -lz >>>>>>> >>>>>>> >>>>>>> >>>>>>> Here is what the binary look like: >>>>>>> >>>>>>> hpcbuild02(salmr0)1181:ldd bin/Linux/3.0/x86_64/ddswriter >>>>>>> linux-vdso.so.1 => (0x00007ffe791a7000) >>>>>>> libz.so.1 => /lib64/libz.so.1 (0x00002aafaab7c000) >>>>>>> libdl.so.2 => /lib64/libdl.so.2 (0x00002aafaad92000) >>>>>>> librt.so.1 => /lib64/librt.so.1 (0x00002aafaaf96000) >>>>>>> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aafab1a0000) >>>>>>> libm.so.6 => /lib64/libm.so.6 (0x00002aafab3bd000) >>>>>>> libc.so.6 => /lib64/libc.so.6 (0x00002aafab636000) >>>>>>> /lib64/ld-linux-x86-64.so.2 (0x00002aafaa95a000) >>>>>>> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aafab9b3000) >>>>>>> hpcbuild02(salmr0)1182:nm bin/Linux/3.0/x86_64/ddswriter|grep darshan >>>>>>> 0000000000482e90 T darshan_clean_file_path >>>>>>> 0000000000483210 t darshan_common_val_compare >>>>>>> 00000000004830c0 T darshan_common_val_counter >>>>>>> 00000000004831a0 t darshan_common_val_walker >>>>>>> 000000000101e860 b darshan_core >>>>>>> 0000000000463f50 t darshan_core_cleanup >>>>>>> 00000000004655e0 T darshan_core_initialize >>>>>>> 0000000000fcfa80 d darshan_core_mutex >>>>>>> 0000000000464720 T darshan_core_register_module >>>>>>> 0000000000464b80 T darshan_core_register_record >>>>>>> 0000000000461c10 T darshan_core_shutdown >>>>>>> 0000000000464840 T darshan_core_unregister_module >>>>>>> 0000000000465310 T darshan_core_unregister_record >>>>>>> 00000000004655b0 T darshan_core_wtime >>>>>>> 0000000000463e40 t darshan_deflate_buffer..0 >>>>>>> 00000000004642b0 t darshan_get_shared_records >>>>>>> 00000000004806a0 T darshan_hash >>>>>>> 0000000000fcfab0 d darshan_mem_alignment >>>>>>> 0000000000fcfaec d darshan_mem_alignment >>>>>>> 0000000000b64848 r darshan_module_names >>>>>>> 0000000000b6487c r darshan_module_versions >>>>>>> 0000000000479ae0 T darshan_mpiio_shutdown_bench_setup >>>>>>> 0000000000fcfa20 D darshan_path_exclusions >>>>>>> 0000000000470250 T darshan_posix_shutdown_bench_setup >>>>>>> 0000000000461750 T darshan_shutdown_bench >>>>>>> 0000000000483230 T darshan_variance_reduce >>>>>>> 0000000000483170 T darshan_walk_common_vals >>>>>>> >>>>>>> >>>>>>> >>>>>>> The problem I am having now is that I donï¿½t get a darshan log file when I run my executable. I configured darshan with this configure flag ï¿½--with-log-path-by-env=DARSHANLOGPATHï¿½. I set that environment variable in my shell to some directory and then run my executable. The executable runs fine but no darshan log file gets generated. >>>>>>> >>>>>>> Any ideas? Thanks in advanced. >>>>>>> >>>>>>> Rene >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 5/20/16, 7:33 AM, "darshan-users-bounces(a)lists.mcs.anl.gov on behalf of Phil Carns" <darshan-users-bounces(a)lists.mcs.anl.gov on behalf of carns(a)mcs.anl.gov> wrote: >>>>>>> >>>>>>>> Hi Rene, >>>>>>>> >>>>>>>> Does mpiifort support the "-show" option (or something similar) to >>>>>>>> display the underlying link command that it is using? >>>>>>>> >>>>>>>> I can describe the manual steps needed to add Darshan support just to >>>>>>>> see if you can get it working, and then we can maybe circle back to why >>>>>>>> the Darshan-generated script is triggering dynamic linking. In general, >>>>>>>> there are two sets of extra link flags that Darshan needs to add to the >>>>>>>> link command. Some should appear before the user-specified libraries in >>>>>>>> the true link command, some should appear after them. On my test box >>>>>>>> they happen to look like this: >>>>>>>> >>>>>>>> pcarns@carns-x1:~/working/install/bin$ darshan-config --pre-ld-flags >>>>>>>> -L/home/pcarns/working/install/lib -ldarshan -lz >>>>>>>> -Wl,@/home/pcarns/working/install/share/ld-opts/darshan-base-ld-opts >>>>>>>> >>>>>>>> pcarns@carns-x1:~/working/install/bin$ darshan-config --post-ld-flags >>>>>>>> -L/home/pcarns/working/install/lib -Wl,--start-group -ldarshan >>>>>>>> -ldarshan-stubs -Wl,--end-group -lz -lrt -lpthread >>>>>>>> >>>>>>>> On most MPI implementations there is also one more library that you have >>>>>>>> to add for MPI function wrapping to work. Darshan-config doesn't add >>>>>>>> that because it is dependent on the MPI implementation. On most versions >>>>>>>> of MPI this is either -lmpifort or -lfmpich. I'm not sure which one >>>>>>>> Intel MPI uses now. >>>>>>>> >>>>>>>> You might be able to do all of that external to mpiifort, but I'm not >>>>>>>> sure. If so, then your link command would look something like this >>>>>>>> (possibly swapping out -lmpifort for -lfmpich or omitting it entirely): >>>>>>>> >>>>>>>> mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o ./ddswriter.revUnversioned -lmpifort `darshan-config --pre-ld-flags` PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost `darshan-config --post-ld-flags` >>>>>>>> >>>>>>>> >>>>>>>> If that doesn't work then you'll need to find out what the underlying >>>>>>>> link command looks like (via -show or similar) and insert it there. >>>>>>>> >>>>>>>> thanks, >>>>>>>> -Phil >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Darshan-users mailing list >>>>>>> Darshan-users(a)lists.mcs.anl.gov >>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users

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No PDF file generation with darshan-summary-per-file.sh
by Suman, Preeti 26 May '16

26 May '16

Hello, I have installed Darshan-3.0.1. I have couple of questions on darshan-summary-per-file.sh. When I run darshan-summary-per-file.sh it gives the following error: #### BEGIN : output of darshan-summary-per-file.sh (using mpi-io-test-x86_64-3.0.1.darshan from darshan-test) $ darshan-summary-per-file.sh mpi-io-test-x86_64-3.0.1.darshan output Status: Generating summary for file 1 of 1: mpi-io-test.tmp.dat ======================================================= Slowest unique file time: 0 Slowest shared file time: 0.033856 Total bytes read and written by app (may be incorrect): 134217728 Total absolute I/O time: 0.033856 **NOTE: above shared and unique file times calculated using MPI-IO timers if MPI-IO interface used on a given file, POSIX timers otherwise. LaTeX generation (phase1) failed [256], aborting summary creation. error log: or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.9 \usepackage {color}^^M ! ==> Fatal error occurred, no output PDF file produced! Transcript written on summary.log. ======================================================= darshan-summary-per-file.sh done. Results can be found in output/*.pdf. #### END : output of darshan-summary-per-file.sh System specification: Kernel Version: Linux 4.0.5-1.el7.elrepo.x86_64 Operating System: CentOS Linux release 7.1.1503 CPU: Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz (Haswell-EP) Architecture:x86_64 Compiler: GCC 5.1.0 MPI: Intel MPI-5.1.2 I have the following questions: a) The color.sty file is located at "/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty". What could be the reason for error? b) I have installed all the prerequisites mentioned in the Darshan-util installation page (zlib, libbz2 development headers and library (libbz2-dev or similar), Perl, pdflatex, gnuplot 4.2 or later, epstopdf), is there any other prerequisite required? c) At the end of the darshan-summary-per-file.sh run, it mentions "Transcript written on summary.log". Where can I locate the log file? I will greatly appreciate your response. Thanks, Preeti

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Re: [Darshan-users] compiling statically with intel toolchain
by Phil Carns 24 May '16

24 May '16

Gnuplot 4.2 should be Ok. I just confirmed that 4.2 patchlevel 6 works with darshan-job-summary.pl on one of our systems. You could try the following to check what happens to gnuplot when it tries to generate the first plot: - add --verbose to the darshan-job-summary.pl command line - look for "verbose: /tmp/1FMc4r0alx" (or something similar) in the first line of output - cd to that directory - run the gnuplot command manually: gnuplot -e "data_file='mpiio-access-hist.dat'; graph_title='MPI-IO Access Sizes {/Times-Bold=32 \263}'; output_file='mpiio-access-hist.eps'" access-hist-eps.gplt In theory it should run cleanly and create a mpiio-access-hist.eps output file. Thanks for your patience getting this stuff working, by the way. I'm not sure what can be done about the Intel MPI Fortran wrapper problem on our end, but if there is a gnuplot issue we should be able to work around it or at least gracefully detect the problem. thanks, -Phil On 05/24/2016 10:37 AM, Salmon, Rene wrote: > Hi, > > hpcbuild02(salmr0)1060:gnuplot -V > gnuplot 4.2 patchlevel 3 > > > > Thanks > Rene > > > > On 5/24/16, 9:35 AM, "Phil Carns" <carns(a)mcs.anl.gov> wrote: > >> Hi Rene, >> >> What version of gnuplot do you have ("gnuplot -V")? >> >> Darshan is supposed to have a safety check for the presence of gnuplot >> and it's version, but the "-e" thing is part of the gnuplot command >> line. Maybe something has gone wrong there. >> >> thanks, >> -Phil >> >> On 05/24/2016 10:21 AM, Salmon, Rene wrote: >>> All, >>> >>> Thank you very much for all the help and info. I now have a working binary that does generate a darshan log file. Your hints where very helpful. What I ended up doing was writing an mpi_init and mpi_finalize wrapper in C that my fortran code calls and that seems to work and now I can generate a darshan log file. >>> >>> I basically just call my_finalize() from my fortran code and that is just this: >>> >>> #include "mpi.h" >>> int my_finalize_(void) >>> { >>> int ier; >>> ier = MPI_Finalize(); >>> return(ier); >>> } >>> >>> >>> Now I just want to analyze the results so I run the darshan-job-summary.pl but I am getting these errors. Any ideas what they mean? >>> >>> hpcbuild02(salmr0)1054:darshan-job-summary.pl ./salmr0_ddswriter_id40315_5-24-32872-5756027388706526063_1.darshan >>> Slowest unique file time: 0.004726 >>> Slowest shared file time: 0.011293 >>> Total bytes read and written by app (may be incorrect): 51934 >>> Total absolute I/O time: 0.016019 >>> **NOTE: above shared and unique file times calculated using MPI-IO timers if MPI-IO interface used on a given file, POSIX timers otherwise. >>> Cannot open load file '-e' >>> line 0: util.c: No such file or directory >>> >>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>> !!! Error: 'posix-access-hist.eps' does not exist! >>> Cannot open load file '-e' >>> line 0: util.c: No such file or directory >>> >>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>> !!! Error: 'file-access-read.eps' does not exist! >>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>> !!! Error: 'file-access-write.eps' does not exist! >>> EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. >>> !!! Error: 'file-access-shared.eps' does not exist! >>> LaTeX generation (phase1) failed [17920], aborting summary creation. >>> error log: >>> Overfull \hbox (18.76118pt too wide) in paragraph at lines 52--52 >>> [][] >>> <time-summary.pdf, id=1, 289.08pt x 252.945pt> <use time-summary.pdf> >>> <op-counts.pdf, id=2, 289.08pt x 252.945pt> <use op-counts.pdf> >>> >>> LaTeX Warning: File `posix-access-hist.pdf' not found on input line 68. >>> >>> >>> !pdfTeX error: pdflatex (file posix-access-hist.pdf): cannot find image file >>> ==> Fatal error occurred, no output PDF file produced! >>> >>> >>> Thanks >>> Rene >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 5/23/16, 5:21 PM, "Harms, Kevin" <harms(a)alcf.anl.gov> wrote: >>> >>>> Rene, >>>> >>>> Your code is making the mpi_init and mpi_finalize call from Fortran correct? You are still hitting the same issue as you noted before which is that the Darshan doesnï¿½t intercept those calls with the Intel MPI implementation. You could specifically add the darshan calls to your Fortran code manually. It isnï¿½t pretty but it should work. This will initialize the library and then it should capture all the calls from your I/O code since that is all in C. >>>> >>>> call mpi_init() >>>> call darshan_core_initialize(%VAL(0), %VAL(0)); >>>> ï¿½ >>>> call darshan_core_shutdown(); >>>> call mpi_finalize() >>>> >>>> depending on the function names, you may need to add an underscore to the end of the names. >>>> >>>> kevin >>>> >>>>> Hi Phil, >>>>> >>>>> Thanks for the info that was helpful. I did manage to link in darshan and MPI statically I had to put in the ï¿½lib.aï¿½ files by hand as the ï¿½darshan-config ï¿½pre/postï¿½ scripts where still trying to link in darshan dynamically. >>>>> Here is the link line I used that seem to generate a binary. >>>>> >>>>> >>>>> mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o /hpcdata/salmr0/mspain/usp2hdf5/dds/bin/Linux/3.0/x86_64/ddswriter.revUnversioned /hpc/tstapps/intel/x86_64/ics-2016.update.1/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.a -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a -lz -Wl,@/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/share/ld-opts/darshan-base-ld-opts svn_version.o PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib -Wl,--start-group /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan-stubs.a -Wl,--end-group -lz >>>>> >>>>> >>>>> >>>>> Here is what the binary look like: >>>>> >>>>> hpcbuild02(salmr0)1181:ldd bin/Linux/3.0/x86_64/ddswriter >>>>> linux-vdso.so.1 => (0x00007ffe791a7000) >>>>> libz.so.1 => /lib64/libz.so.1 (0x00002aafaab7c000) >>>>> libdl.so.2 => /lib64/libdl.so.2 (0x00002aafaad92000) >>>>> librt.so.1 => /lib64/librt.so.1 (0x00002aafaaf96000) >>>>> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aafab1a0000) >>>>> libm.so.6 => /lib64/libm.so.6 (0x00002aafab3bd000) >>>>> libc.so.6 => /lib64/libc.so.6 (0x00002aafab636000) >>>>> /lib64/ld-linux-x86-64.so.2 (0x00002aafaa95a000) >>>>> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aafab9b3000) >>>>> hpcbuild02(salmr0)1182:nm bin/Linux/3.0/x86_64/ddswriter|grep darshan >>>>> 0000000000482e90 T darshan_clean_file_path >>>>> 0000000000483210 t darshan_common_val_compare >>>>> 00000000004830c0 T darshan_common_val_counter >>>>> 00000000004831a0 t darshan_common_val_walker >>>>> 000000000101e860 b darshan_core >>>>> 0000000000463f50 t darshan_core_cleanup >>>>> 00000000004655e0 T darshan_core_initialize >>>>> 0000000000fcfa80 d darshan_core_mutex >>>>> 0000000000464720 T darshan_core_register_module >>>>> 0000000000464b80 T darshan_core_register_record >>>>> 0000000000461c10 T darshan_core_shutdown >>>>> 0000000000464840 T darshan_core_unregister_module >>>>> 0000000000465310 T darshan_core_unregister_record >>>>> 00000000004655b0 T darshan_core_wtime >>>>> 0000000000463e40 t darshan_deflate_buffer..0 >>>>> 00000000004642b0 t darshan_get_shared_records >>>>> 00000000004806a0 T darshan_hash >>>>> 0000000000fcfab0 d darshan_mem_alignment >>>>> 0000000000fcfaec d darshan_mem_alignment >>>>> 0000000000b64848 r darshan_module_names >>>>> 0000000000b6487c r darshan_module_versions >>>>> 0000000000479ae0 T darshan_mpiio_shutdown_bench_setup >>>>> 0000000000fcfa20 D darshan_path_exclusions >>>>> 0000000000470250 T darshan_posix_shutdown_bench_setup >>>>> 0000000000461750 T darshan_shutdown_bench >>>>> 0000000000483230 T darshan_variance_reduce >>>>> 0000000000483170 T darshan_walk_common_vals >>>>> >>>>> >>>>> >>>>> The problem I am having now is that I donï¿½t get a darshan log file when I run my executable. I configured darshan with this configure flag ï¿½--with-log-path-by-env=DARSHANLOGPATHï¿½. I set that environment variable in my shell to some directory and then run my executable. The executable runs fine but no darshan log file gets generated. >>>>> >>>>> Any ideas? Thanks in advanced. >>>>> >>>>> Rene >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 5/20/16, 7:33 AM, "darshan-users-bounces(a)lists.mcs.anl.gov on behalf of Phil Carns" <darshan-users-bounces(a)lists.mcs.anl.gov on behalf of carns(a)mcs.anl.gov> wrote: >>>>> >>>>>> Hi Rene, >>>>>> >>>>>> Does mpiifort support the "-show" option (or something similar) to >>>>>> display the underlying link command that it is using? >>>>>> >>>>>> I can describe the manual steps needed to add Darshan support just to >>>>>> see if you can get it working, and then we can maybe circle back to why >>>>>> the Darshan-generated script is triggering dynamic linking. In general, >>>>>> there are two sets of extra link flags that Darshan needs to add to the >>>>>> link command. Some should appear before the user-specified libraries in >>>>>> the true link command, some should appear after them. On my test box >>>>>> they happen to look like this: >>>>>> >>>>>> pcarns@carns-x1:~/working/install/bin$ darshan-config --pre-ld-flags >>>>>> -L/home/pcarns/working/install/lib -ldarshan -lz >>>>>> -Wl,@/home/pcarns/working/install/share/ld-opts/darshan-base-ld-opts >>>>>> >>>>>> pcarns@carns-x1:~/working/install/bin$ darshan-config --post-ld-flags >>>>>> -L/home/pcarns/working/install/lib -Wl,--start-group -ldarshan >>>>>> -ldarshan-stubs -Wl,--end-group -lz -lrt -lpthread >>>>>> >>>>>> On most MPI implementations there is also one more library that you have >>>>>> to add for MPI function wrapping to work. Darshan-config doesn't add >>>>>> that because it is dependent on the MPI implementation. On most versions >>>>>> of MPI this is either -lmpifort or -lfmpich. I'm not sure which one >>>>>> Intel MPI uses now. >>>>>> >>>>>> You might be able to do all of that external to mpiifort, but I'm not >>>>>> sure. If so, then your link command would look something like this >>>>>> (possibly swapping out -lmpifort for -lfmpich or omitting it entirely): >>>>>> >>>>>> mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o ./ddswriter.revUnversioned -lmpifort `darshan-config --pre-ld-flags` PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost `darshan-config --post-ld-flags` >>>>>> >>>>>> >>>>>> If that doesn't work then you'll need to find out what the underlying >>>>>> link command looks like (via -show or similar) and insert it there. >>>>>> >>>>>> thanks, >>>>>> -Phil >>>>>> >>>>> _______________________________________________ >>>>> Darshan-users mailing list >>>>> Darshan-users(a)lists.mcs.anl.gov >>>>> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users

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Re: [Darshan-users] compiling statically with intel toolchain
by Phil Carns 24 May '16

24 May '16

Hi Rene, What version of gnuplot do you have ("gnuplot -V")? Darshan is supposed to have a safety check for the presence of gnuplot and it's version, but the "-e" thing is part of the gnuplot command line. Maybe something has gone wrong there. thanks, -Phil On 05/24/2016 10:21 AM, Salmon, Rene wrote: > All, > > Thank you very much for all the help and info. I now have a working binary that does generate a darshan log file. Your hints where very helpful. What I ended up doing was writing an mpi_init and mpi_finalize wrapper in C that my fortran code calls and that seems to work and now I can generate a darshan log file. > > I basically just call my_finalize() from my fortran code and that is just this: > > #include "mpi.h" > int my_finalize_(void) > { > int ier; > ier = MPI_Finalize(); > return(ier); > } > > > Now I just want to analyze the results so I run the darshan-job-summary.pl but I am getting these errors. Any ideas what they mean? > > hpcbuild02(salmr0)1054:darshan-job-summary.pl ./salmr0_ddswriter_id40315_5-24-32872-5756027388706526063_1.darshan > Slowest unique file time: 0.004726 > Slowest shared file time: 0.011293 > Total bytes read and written by app (may be incorrect): 51934 > Total absolute I/O time: 0.016019 > **NOTE: above shared and unique file times calculated using MPI-IO timers if MPI-IO interface used on a given file, POSIX timers otherwise. > Cannot open load file '-e' > line 0: util.c: No such file or directory > > EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. > !!! Error: 'posix-access-hist.eps' does not exist! > Cannot open load file '-e' > line 0: util.c: No such file or directory > > EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. > !!! Error: 'file-access-read.eps' does not exist! > EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. > !!! Error: 'file-access-write.eps' does not exist! > EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al. > !!! Error: 'file-access-shared.eps' does not exist! > LaTeX generation (phase1) failed [17920], aborting summary creation. > error log: > Overfull \hbox (18.76118pt too wide) in paragraph at lines 52--52 > [][] > <time-summary.pdf, id=1, 289.08pt x 252.945pt> <use time-summary.pdf> > <op-counts.pdf, id=2, 289.08pt x 252.945pt> <use op-counts.pdf> > > LaTeX Warning: File `posix-access-hist.pdf' not found on input line 68. > > > !pdfTeX error: pdflatex (file posix-access-hist.pdf): cannot find image file > ==> Fatal error occurred, no output PDF file produced! > > > Thanks > Rene > > > > > > > > > > > On 5/23/16, 5:21 PM, "Harms, Kevin" <harms(a)alcf.anl.gov> wrote: > >> Rene, >> >> Your code is making the mpi_init and mpi_finalize call from Fortran correct? You are still hitting the same issue as you noted before which is that the Darshan doesnï¿½t intercept those calls with the Intel MPI implementation. You could specifically add the darshan calls to your Fortran code manually. It isnï¿½t pretty but it should work. This will initialize the library and then it should capture all the calls from your I/O code since that is all in C. >> >> call mpi_init() >> call darshan_core_initialize(%VAL(0), %VAL(0)); >> ï¿½ >> call darshan_core_shutdown(); >> call mpi_finalize() >> >> depending on the function names, you may need to add an underscore to the end of the names. >> >> kevin >> >>> Hi Phil, >>> >>> Thanks for the info that was helpful. I did manage to link in darshan and MPI statically I had to put in the ï¿½lib.aï¿½ files by hand as the ï¿½darshan-config ï¿½pre/postï¿½ scripts where still trying to link in darshan dynamically. >>> Here is the link line I used that seem to generate a binary. >>> >>> >>> mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o /hpcdata/salmr0/mspain/usp2hdf5/dds/bin/Linux/3.0/x86_64/ddswriter.revUnversioned /hpc/tstapps/intel/x86_64/ics-2016.update.1/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.a -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a -lz -Wl,@/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/share/ld-opts/darshan-base-ld-opts svn_version.o PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib -Wl,--start-group /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan-stubs.a -Wl,--end-group -lz >>> >>> >>> >>> Here is what the binary look like: >>> >>> hpcbuild02(salmr0)1181:ldd bin/Linux/3.0/x86_64/ddswriter >>> linux-vdso.so.1 => (0x00007ffe791a7000) >>> libz.so.1 => /lib64/libz.so.1 (0x00002aafaab7c000) >>> libdl.so.2 => /lib64/libdl.so.2 (0x00002aafaad92000) >>> librt.so.1 => /lib64/librt.so.1 (0x00002aafaaf96000) >>> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aafab1a0000) >>> libm.so.6 => /lib64/libm.so.6 (0x00002aafab3bd000) >>> libc.so.6 => /lib64/libc.so.6 (0x00002aafab636000) >>> /lib64/ld-linux-x86-64.so.2 (0x00002aafaa95a000) >>> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aafab9b3000) >>> hpcbuild02(salmr0)1182:nm bin/Linux/3.0/x86_64/ddswriter|grep darshan >>> 0000000000482e90 T darshan_clean_file_path >>> 0000000000483210 t darshan_common_val_compare >>> 00000000004830c0 T darshan_common_val_counter >>> 00000000004831a0 t darshan_common_val_walker >>> 000000000101e860 b darshan_core >>> 0000000000463f50 t darshan_core_cleanup >>> 00000000004655e0 T darshan_core_initialize >>> 0000000000fcfa80 d darshan_core_mutex >>> 0000000000464720 T darshan_core_register_module >>> 0000000000464b80 T darshan_core_register_record >>> 0000000000461c10 T darshan_core_shutdown >>> 0000000000464840 T darshan_core_unregister_module >>> 0000000000465310 T darshan_core_unregister_record >>> 00000000004655b0 T darshan_core_wtime >>> 0000000000463e40 t darshan_deflate_buffer..0 >>> 00000000004642b0 t darshan_get_shared_records >>> 00000000004806a0 T darshan_hash >>> 0000000000fcfab0 d darshan_mem_alignment >>> 0000000000fcfaec d darshan_mem_alignment >>> 0000000000b64848 r darshan_module_names >>> 0000000000b6487c r darshan_module_versions >>> 0000000000479ae0 T darshan_mpiio_shutdown_bench_setup >>> 0000000000fcfa20 D darshan_path_exclusions >>> 0000000000470250 T darshan_posix_shutdown_bench_setup >>> 0000000000461750 T darshan_shutdown_bench >>> 0000000000483230 T darshan_variance_reduce >>> 0000000000483170 T darshan_walk_common_vals >>> >>> >>> >>> The problem I am having now is that I donï¿½t get a darshan log file when I run my executable. I configured darshan with this configure flag ï¿½--with-log-path-by-env=DARSHANLOGPATHï¿½. I set that environment variable in my shell to some directory and then run my executable. The executable runs fine but no darshan log file gets generated. >>> >>> Any ideas? Thanks in advanced. >>> >>> Rene >>> >>> >>> >>> >>> >>> >>> On 5/20/16, 7:33 AM, "darshan-users-bounces(a)lists.mcs.anl.gov on behalf of Phil Carns" <darshan-users-bounces(a)lists.mcs.anl.gov on behalf of carns(a)mcs.anl.gov> wrote: >>> >>>> Hi Rene, >>>> >>>> Does mpiifort support the "-show" option (or something similar) to >>>> display the underlying link command that it is using? >>>> >>>> I can describe the manual steps needed to add Darshan support just to >>>> see if you can get it working, and then we can maybe circle back to why >>>> the Darshan-generated script is triggering dynamic linking. In general, >>>> there are two sets of extra link flags that Darshan needs to add to the >>>> link command. Some should appear before the user-specified libraries in >>>> the true link command, some should appear after them. On my test box >>>> they happen to look like this: >>>> >>>> pcarns@carns-x1:~/working/install/bin$ darshan-config --pre-ld-flags >>>> -L/home/pcarns/working/install/lib -ldarshan -lz >>>> -Wl,@/home/pcarns/working/install/share/ld-opts/darshan-base-ld-opts >>>> >>>> pcarns@carns-x1:~/working/install/bin$ darshan-config --post-ld-flags >>>> -L/home/pcarns/working/install/lib -Wl,--start-group -ldarshan >>>> -ldarshan-stubs -Wl,--end-group -lz -lrt -lpthread >>>> >>>> On most MPI implementations there is also one more library that you have >>>> to add for MPI function wrapping to work. Darshan-config doesn't add >>>> that because it is dependent on the MPI implementation. On most versions >>>> of MPI this is either -lmpifort or -lfmpich. I'm not sure which one >>>> Intel MPI uses now. >>>> >>>> You might be able to do all of that external to mpiifort, but I'm not >>>> sure. If so, then your link command would look something like this >>>> (possibly swapping out -lmpifort for -lfmpich or omitting it entirely): >>>> >>>> mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o ./ddswriter.revUnversioned -lmpifort `darshan-config --pre-ld-flags` PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost `darshan-config --post-ld-flags` >>>> >>>> >>>> If that doesn't work then you'll need to find out what the underlying >>>> link command looks like (via -show or similar) and insert it there. >>>> >>>> thanks, >>>> -Phil >>>> >>> >>> _______________________________________________ >>> Darshan-users mailing list >>> Darshan-users(a)lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users

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Re: [Darshan-users] compiling statically with intel toolchain
by Phil Carns 24 May '16

24 May '16

Hi Rene, Does mpiifort support the "-show" option (or something similar) to display the underlying link command that it is using? I can describe the manual steps needed to add Darshan support just to see if you can get it working, and then we can maybe circle back to why the Darshan-generated script is triggering dynamic linking. In general, there are two sets of extra link flags that Darshan needs to add to the link command. Some should appear before the user-specified libraries in the true link command, some should appear after them. On my test box they happen to look like this: pcarns@carns-x1:~/working/install/bin$ darshan-config --pre-ld-flags -L/home/pcarns/working/install/lib -ldarshan -lz -Wl,@/home/pcarns/working/install/share/ld-opts/darshan-base-ld-opts pcarns@carns-x1:~/working/install/bin$ darshan-config --post-ld-flags -L/home/pcarns/working/install/lib -Wl,--start-group -ldarshan -ldarshan-stubs -Wl,--end-group -lz -lrt -lpthread On most MPI implementations there is also one more library that you have to add for MPI function wrapping to work. Darshan-config doesn't add that because it is dependent on the MPI implementation. On most versions of MPI this is either -lmpifort or -lfmpich. I'm not sure which one Intel MPI uses now. You might be able to do all of that external to mpiifort, but I'm not sure. If so, then your link command would look something like this (possibly swapping out -lmpifort for -lfmpich or omitting it entirely): mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o ./ddswriter.revUnversioned -lmpifort `darshan-config --pre-ld-flags` PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost `darshan-config --post-ld-flags` If that doesn't work then you'll need to find out what the underlying link command looks like (via -show or similar) and insert it there. thanks, -Phil On 05/18/2016 05:21 PM, Salmon, Rene wrote: > Hi, > > >> I think this means you are using dynamic linking. You could try darshan using the dynamic linking method that uses LD_PRELOAD. >> >> http://www.mcs.anl.gov/research/projects/darshan/docs/darshan-runtime.html#… > I tried LD_PRELOAD and that did not do much for me. > > We actually want to link in MPI and Darshan statically. We typically link MPI statically with intel MPI by just adding the ï¿½-static_mpiï¿½ option to mpiifort. Unfortunately the darshan script calls ifort directly and as far as I can tell it is linking in MPI dynamically. What would I need to add to my link line to get darshan compiled statically? Here is my link line: > > mpiifort -DLinux -Dx86_64 -DINTEL -DCompLevel16 -DX86_64 -D__x86_64__ -static-intel -static_mpi -DOpenMP -openmp -DSWAP -O3 -g -o ./ddswriter.revUnversioned PartitionLayout_mod.o ddswriter.o -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -ldds_r3 -lgio -lfhost > > >> Yes, possibly. Intel may have changed their setup but unlikely. I believe the issue here is that that the Intel Fortran MPI functions call the PMPI_* routines directly and thus can not be intercepted unless the specific Fortran interface is intercepted. Do you do I/O from FORTAN directly or are you using an I/O library? > > We do all IO using a library written in C. We do not do any IO using fortran. > > Thanks for the help > Rene > > > _______________________________________________ > Darshan-users mailing list > Darshan-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/darshan-users

4 4

Darshan 3.0.1 now available
by Shane Snyder 20 May '16

20 May '16

Darshan users, Darshan version 3.0.1 is now available for download. This version contains a number of bug fixes and enhancements to Darshan 3.0.0. For reference, the complete list of changes for this release is: * bug fix in darshan logutil mount parsing code that was causing file paths to be matched to the first mount point with a common prefix rather than the one with the longest common prefix * bug fix in the darshan-util bzip2 configure check that was accidentally overwriting Darshan’s LDFLAGS * minor bug fixes to IO start time counters in all modules to set IO start time to the actual first start time rather than the first IO op to complete * update darshan-util perl scripts to get perl bin from user’s path, rather than from /usr/lib (reported by Kay Thust) * update Darshan’s fortran and cxx compiler wrapper generators to automatically detect MPICH library names on BG/Q * bug fix for calculating Darshan’s agg_perf_by_slowest performance metric correctly * add performance estimate info to darshan-job-summary graph We have tested this release on multiple platforms, but please let us know if you have any issues or questions. You can report issues directly using Darshan’s GitLab page <https://xgitlab.cels.anl.gov/darshan/darshan> or by using this mailing list. The release tarball can be downloaded HERE <http://press3.mcs.anl.gov/darshan/download/>. Documentation for this version of Darshan can be found HERE <http://press3.mcs.anl.gov/darshan/documentation/>. Thanks! --Darshan team

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Re: [Darshan-users] compiling statically with intel toolchain
by Harms, Kevin 18 May '16

18 May '16

Rene, are you using either the darshan generated compiler wrappers or trying to use the MPICH profiling hooks? Can you add the '-show' option to you link command. Instead of linking it will display the full link command that the wrapper is executing. kevin >Hi, > >I am trying to compile darshan statically into my application using Intel’s fortran compiler and MPI library. When I do so I get this error message: > > >-L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib -ldds_r3 -lgio -lfhost -Wl,-Bstatic -ldarshan -ldarshan-stubs -lz -Wl,-Bdynamic > > >/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a(darshan-posix.o): In function `__wrap_open': >/hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:378: undefined reference to `__real_open' >/hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:384: undefined reference to `__real_open' > >/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a(darshan-posix.o): In function `__wrap_open64': > >/hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:412: undefined reference to `__real_open64' > >/hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:418: undefined reference to `__real_open64' > >/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a(darshan-posix.o): In function `__wrap_creat': > >… > > >the real_open routines seem to be in the libdarshan library: > >nm /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a |grep real_open > > U __real_open > U __real_open64 > > > >Any ideas? > >Thanks >Rene > >

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compiling statically with intel toolchain
by Salmon, Rene 17 May '16

17 May '16

Hi, I am trying to compile darshan statically into my application using Intel’s fortran compiler and MPI library. When I do so I get this error message: -L/tstapps/asi/src/dds/lib/Linux/3.0/x86_64/Intel-16.0.1.150MPI5.1.2MKL11.3.1 -L/hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib -ldds_r3 -lgio -lfhost -Wl,-Bstatic -ldarshan -ldarshan-stubs -lz -Wl,-Bdynamic /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a(darshan-posix.o): In function `__wrap_open': /hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:378: undefined reference to `__real_open' /hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:384: undefined reference to `__real_open' /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a(darshan-posix.o): In function `__wrap_open64': /hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:412: undefined reference to `__real_open64' /hpc/tstapps/src/darshan/darshan-3.0.0/darshan-runtime/lib/darshan-posix.c:418: undefined reference to `__real_open64' /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a(darshan-posix.o): In function `__wrap_creat': … the real_open routines seem to be in the libdarshan library: nm /hpc/tstapps/SLES/3.0/x86_64/darshan/3.0.0/lib/libdarshan.a |grep real_open U __real_open U __real_open64 Any ideas? Thanks Rene

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darshan-job-summary.pl interpreter
by Kay Thust 04 May '16

04 May '16

Dear all, It would be nice if the interpreter for darshan-job-summary.pl could be something picked from the environment, like #!/usr/bin/env perl instead of #!/usr/bin/perl Since our site does not provide, e.g. the LaTeX package for the system Perl but for the one we install as a module, we rely on not using the Perl interpreter in /usr/bin but in our custom path. Thanks and best regards, Kay -- Dr. Kay Thust Juelich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Juelich GmbH ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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technical report on Darshan 3.0.0 performance
by Shane Snyder 03 May '16

03 May '16

Darshan users, As part of our transition to the new modularized version of Darshan (3.0.0), we have published a technical report evaluating its performance on Edison, a production Cray XC30 system at NERSC. This technical report primarily serves as validation that Darshan’s performance remains suitable for full-time deployment on production HPC systems, but it also provides some additional background that may be useful in understanding the design changes made to Darshan’s runtime library and log file format. Our results indicate that Darshan’s new design is still lightweight enough to run full-time on production systems with little to no impact on the performance of instrumented applications. A PDF for this technical report can be found HERE <http://www.mcs.anl.gov/papers/MCS_TM_362_1.pdf>. --Darshan team

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