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HYPHY Package >> HyPhy bugs >> compiling HYPHY on powerpc-ibm-aix5.2.0.0 http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1116514305 Message started by avilella on May 19th, 2005 at 7:51am |
Title: compiling HYPHY on powerpc-ibm-aix5.2.0.0 Post by avilella on May 19th, 2005 at 7:51am
Hi all,
I'm trying to compile HYPHY on a nice powerpc-ibm-aix5.2.0.0 with lots of nodes to take advantage of parallelization, but there seems to be a problem with library versions: ---- sp2n1 >sh build.sh SP AIX build.sh[11]: ==: 0403-012 A test command parameter is not valid. build.sh[16]: ==: 0403-012 A test command parameter is not valid. COMPILER_FLAGS= -w -c -O3 -fpermissive -I/scratch_tmp/jrozas/hyphy_latest/HYPHY_Source/Source -I/scratch_tmp/jrozas/hyphy_latest/HYPHY_Source/Source/SQLite +--------------------------------------+ |Building a single threaded HYPHYKernel| +--------------------------------------+ Building HYNetInterface.cpp Complete Building Net.cpp Complete Building baseobj.cpp Complete Building batchlan.cpp Complete Building batchlan2.cpp Complete Building calcnode.cpp Complete Building category.cpp Complete Building error.cpp Complete Building fisher_exact.cpp Complete Building likefunc.cpp Complete Building list.cpp Complete Building matrix.cpp Complete Building nexus.cpp Complete Building parser.cpp Complete Building parser2.cpp Complete Building polynoml.cpp Complete Building regex.cpp Complete Building sequence.cpp Complete Building site.cpp Complete Building strings.cpp Complete Building main-unix.cp In file included from main-unix.cp:29: /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:2031: declaration of C function `int mvwprintw(WINDOW*, int, int, ...)' conflicts with /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:401: previous declaration `int mvwprintw(WINDOW*, int, int, char*, ...)' here /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:2032: declaration of C function `int mvwscanw(WINDOW*, int, int, ...)' conflicts with /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:402: previous declaration `int mvwscanw(WINDOW*, int, int, char*, ...)' here /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:2034: declaration of C function `int overwrite(WINDOW*, WINDOW*)' conflicts with /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:1293: previous declaration `int overwrite(const WINDOW*, WINDOW*)' here /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:2037: declaration of C function `int waddstr(WINDOW*, char*)' conflicts with /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:1299: previous declaration `int waddstr(WINDOW*, const char*)' here /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:2047: declaration of C function `int wprintw(WINDOW*, ...)' conflicts with /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:404: previous declaration `int wprintw(WINDOW*, char*, ...)' here /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:2049: declaration of C function `int wscanw(WINDOW*, ...)' conflicts with /usr/local/gcc3.1/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.1/include/curses.h:404: previous declaration `int wscanw(WINDOW*, char*, ...)' here main-unix.cp:40:31: curl/curl.h: No such file or directory main-unix.cp: In function `bool Get_a_URL(_String&, _String*)': main-unix.cp:396: `CURL' undeclared (first use this function) main-unix.cp:396: (Each undeclared identifier is reported only once for each function it appears in.) main-unix.cp:396: `curl' undeclared (first use this function) main-unix.cp:397: `CURLcode' undeclared (first use this function) main-unix.cp:397: parse error before `;' token main-unix.cp:398: `curl_easy_init' undeclared (first use this function) main-unix.cp:401: `CURL_ERROR_SIZE' undeclared (first use this function) main-unix.cp:419: `CURLOPT_URL' undeclared (first use this function) main-unix.cp:419: `curl_easy_setopt' undeclared (first use this function) main-unix.cp:420: `CURLOPT_ERRORBUFFER' undeclared (first use this function) main-unix.cp:420: `cErr' undeclared (first use this function) main-unix.cp:422: `CURLOPT_FILE' undeclared (first use this function) main-unix.cp:427: `CURLOPT_USERAGENT' undeclared (first use this function) main-unix.cp:429: `CURLOPT_WRITEFUNCTION' undeclared (first use this function) main-unix.cp:434: `CURLOPT_NOPROGRESS' undeclared (first use this function) main-unix.cp:436: `res' undeclared (first use this function) main-unix.cp:436: `curl_easy_perform' undeclared (first use this function) main-unix.cp:437: `curl_easy_cleanup' undeclared (first use this function) Error during compilation ---- It seems that the if's in line 11 and 16 fail, then tries to use gcc instead of xlc. Later, it fails with mvwprintw function: don't know if it is a version problem or what. This computer has a: /usr/local/gcc3.3.4/lib/gcc-lib/powerpc-ibm-aix5.2.0.0/3.3.4/include/curses.h ... instead of the gcc3.1 version. Will the compilation improve with gcc3.3.4 version? Does hyphy depends on a specific version of curses, curl, ssl, crypto, pthread and/or mpi/mpich. Thanks in advance, Albert. |
Title: Re: compiling HYPHY on powerpc-ibm-aix5.2.0.0 Post by Sergei on May 19th, 2005 at 8:41am
Dear Albert,
I have successfully compiled HyPhy on an AIX machine using xlc, but the current build script doesn't support it and the source needs to be #ifdefed in 2 or 3 places for xlc to accept it. I will modify the scripts and insert appropriate ifdefs and get back to you later today. Cheers, Sergei |
Title: Re: compiling HYPHY on powerpc-ibm-aix5.2.0.0 Post by Sergei on May 19th, 2005 at 11:07am
Dear Albert,
I have updated the build.sh script to compile out of the box on an AIX machine with xlC (32 bit mode - no noticeable difference in performance with 64 bit in my testing). Download the latest version and run $bash build.sh MPI or $bash build.sh MP2 Let me know if this works. Cheers, Sergei |
Title: Re: compiling HYPHY on powerpc-ibm-aix5.2.0.0 Post by avilella on May 20th, 2005 at 2:17am
The AIX is still not recognized in lines 12 and 17 but I could manually tweak build.sh to a build.sh.aix.mpi.
I'm having some strange xlC troubles with some of the files like batchlan.cpp and likefunc.cpp: Only this prompt appears: xlC: 1501-224 fatal error in /usr/vac/exe/ipa: signal 24 received ...still investigating. BTW: there are 2 or 3 warning that pop up with xlC that may be easily fixed initializing the vars: sp2n1 >sh build.aix.mpi COMPILER=xlC, xlc COMPILER_FLAGS= -c -qchar=signed -O5 -D__HYPHY_NO_CURL__ +-----------------------------------------------------------+ |Building a single-threaded HYPHYKernelMPI for MPI | +-----------------------------------------------------------+ File HYNetInterface.cpp is up to date File Net.cpp is up to date File baseobj.cpp is up to date File batchlan.cpp is up to date File batchlan2.cpp is up to date File calcnode.cpp is up to date Building category.cpp 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Complete Building error.cpp Complete Building fisher_exact.cpp 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Complete Building likefunc.cpp "likefunc.cpp", line 5978.45: 1540-1102 (W) "D" might be used before it is set. "likefunc.cpp", line 6239.45: 1540-1102 (W) "D" might be used before it is set. "likefunc.cpp", line 6495.26: 1540-1102 (W) "lastError" might be used before it is set. [...] Building polynoml.cpp "polynoml.cpp", line 1023.81: 1540-1102 (W) "term2" might be used before it is set. 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Complete Building regex.cpp Complete Building sequence.cpp "sequence.cpp", line 606.47: 1540-1102 (W) "pos1" might be used before it is set. 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Complete [...] |
Title: Re: compiling HYPHY on powerpc-ibm-aix5.2.0.0 Post by Sergei on May 20th, 2005 at 7:42am
Dear Albert,
Quote:
Try calling $bash build.sh instead of $sh build.sh. Older 'sh' versions may not like the string comparison '==' syntax. Try to replace == with -eq (might be more compatible) and see if that works. Quote:
batchlan.cpp and likefunc.cpp have large functions which xlC may need loads of memory to optimize at -O5. Try -O3 (or -O2) instead maybe? Quote:
My xlC gives me the same warnings; I checked the code to make sure those weren't bugs, which they aren't; all the warnings are in legacy functions that no longer are used in the main code, and should be pruned out - I am going to do that in the next maintenance release. Best, Sergei |
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