Please keep all discussions on the mailing list! Also, I'm also CC-ing to the gmx-devel list, maybe somebody over there has an better what causes your CMake issue.
>>> //Flags used by the compiler during all build types >>> CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 ' >>> >>> //Flags used by the compiler during release builds. >>> CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 -DNDEBUG >>> ... >>> These are obviously the wrong flags for the detected architecture, >>> sse2 is no longer available and so are the the mtune architectures. >> >> Indeed, some of those flags are wrong (CXX -std=gnu99), others simply >> outdated (-mtune=itanium2). There are plans to correct these issues >> for 4.6, but let's agree on the fact that they are not show-stoppers >> (FYI you won't get more than a few percent speedup with the right >> compiler options, the most I've seen is ~5%.) > > OK, I was under the impression it would be simple to correct that - > independend of gains if any. Theoretically it is, but in practice not so much. Keeping up with the ever changing compiler options - especially the architecture-related optimization flags - is not a fun job. We'll try to improve these aspects of the CMkake build system the next release. >> If you want to get rid of them, the solution is pretty simple: just >> remove the offending options and pick new ones if you think they work >> better for you. > > That involves hand-editing the CMakeCache which may be no less > bothersome than enduring the warnings ;-) You can use ccmake (or cmake-gui), they will make your life easier. Otherwise, editing the cache is nowhere near as difficult as it sounds. ;) >> However, I'm not sure what do you mean by "sse2 is no longer >> available"? Of course it is, both the Intel Compiler and the majority >> of current processors support it. Also, -mtune=core2 is perfectly >> valid as is -msse2. > > I checked that with the documentation on the Intel site and > the code generation options written out by the compiler (as > help info). On the Intel site, -msse2 and -mtune=core2 are > still listed as valid, whereas they aren't mentioned in the > help provided by the compiler I installed. Maybe they are > redundant with the Intel64-compiler and set by default > (not entirely sure). Bottom line: you are right here, I > missed some information. i) Indded the "-msse2" is redundant. From the icc man page: "On Linux systems, if neither -x nor -m is specified, the default is -msse2." ii) Nope, the default as usually is -mtune=generic on "IA-32" and "Intel 64" - as Intel likes to call them. Btw, core2 is essentially equivalent with -xSSSE3. Depending on the processors you intend to run on you can try -xSSE4.1 or -xSSE4.2, but I doubt you'll see a noticeable difference. >>> CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 ' >> >> As Mark said, SSE3 won't help you in any noticeable way. > > The only 'help' I envisioned here was to avoid screen cluttering > by loads of warnings. mMy suggested 'fixes' weren't really fixes, > as I can see now. In my own development work, I can't stand > pages of recurring warning messages ;-) So I probably > overreacted here ... Sure, warnings are not nice and we dislike them as well. That's why these issues will be corrected in the future. >>> But the install is broken. On `make install-mdrun`, the scripts would >>> remove any library from "src/gmxlib/CMakeFiles/CMakeRelink.dir" >>> and bail out with the error below. Even if you copy the libraries >>> by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun >>> before trying to link with them. >> >> Now that is a bug. I'd appreciate if you could enter it in >> redmine.gromacs.org withe all details on how to reproduce it! > > I didn't do that until now but examined this further. There is already > an identical error posted by some other researcher (as you know): > http://www.mail-archive.com/gmx-users@gromacs.org/msg39228.html > > I was able to replicate the error somehow on a different machine without > any intel compiler around (when building with -DGMX_MPI=ON and cmake). > > Gromacs 4.5.5: autoconf/configure on SuSE 11.4/x64 on i7 > ---------------------------------------------------------------- > icc/64-12.1.0 gcc/x64/4.5.1 > intThread OK OK > MPI(1.3.2) OK OK > > > Gromacs 4.5.5: cmake 2.8.3 on SuSE 11.4/x64 on i7 > ---------------------------------------------------------------- > icc/64-12.1.0 gcc/x64/4.5.1 > intThread error OK > MPI(1.3.2) error error > > > Gromacs 4.5.5: autoconf/configure on SuSE 11.4/x64 on Phenom/X4 > ---------------------------------------------------------------- > gcc/x64/4.5.1 gcc/x64/4.6.1 > intThread OK OK > MPI(1.3.2) OK OK > > > Gromacs 4.5.5: cmake 2.8.3 on SuSE 11.4/x64 on Phenom/X4 > ---------------------------------------------------------------- > gcc/x64/4.5.1 gcc/x64/4.6.1 > intThread OK OK > MPI(1.3.2) error error > > > Gromacs/git (2011-10-18): cmake 2.8.3 on SuSE 11.4/x64 on Phenom/X4 > ------------------------------------------------------------------- > gcc/x64/4.5.1 gcc/x64/4.6.1 > intThread error error > MPI(1.3.2) error error > > > Notes: - the MPI is openmpi out-out-the-box w/SuSE 11.4 > - Gromacs/git - w/autoconf was not tested > - Intel-Compiler on AMD Phenom N/A > - Gromacs/git failed w/compile error > on Boost(?) -> src/gromacs/analysisdata/modules/plot.cpp:60 > boost::mpl::aux::template_arity<mpl_::na>::value’ is not a > valid template argument for type ‘int’ because it is a > non-constant expression (many following) > - Boost version is 1.4.6 (actual version) > > Resumé: > - autoconf succeeds in almost all cases with any compiler > - cmake fails in almost all cases except the simplest ones (cmake > ../gromacs-src) > > I really don't know what to make out of this. Me neither, but let's try to figure it out. First of all, your OpenMPI is quite outdated; as the build-generation-time message warns OpenMPI <v1.4.1 has known issues. However, I've just tried gcc 4.6.0 + OpenMPI 1.3 with cmake 2.6.4 as well as 2.8.2 and in both cases my installation went just fine. Although I didn't remember seeing you full command line call to CMake, I tried to replicate a quite common scenario: build & install full Gromacs with MPI off and "threads" on, then build & install mdrun with MPI. Here are my command lines: CMAKE_PREFIX_PATH=/my/path/to/fftw3 cmake ../ -DGMX_MPI=OFF -DCMAKE_INSTALL_PREFIX=/tmp/gromacs-4.5 && make -j6 && make install CMAKE_PREFIX_PATH=/my/path/to/fftw3 cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/tmp/gromacs-4.5 && make mdrun -j6 && make install-mdrun Could you please run the above commands and see what you get. If make install-mdrun still fails, please attach your CMakeCache.txt so we can take a look at it. Cheers, -- Szilárd -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
