Hi all, Thanks to everybody who has contributed over the past couple of days on the various bulletin boards I have posted to. As is always the case, the solution was quite simple but completely passed me by. I'm going to use Mac inexperience as an excuse here... :-)
So the original problem was not being able to compile a working executable of CNS v1.21 from source on Mac OSX 10.6.3. The reason for compiling from source is because in order to run CNS from Aria 2.3, a program used in NMR automated peak assignment and structure calculation, CNS needs to be recompiled with Aria-specific source code. With fink-installed gfortran/gcc 4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. With fink-installed 4.4, CNS compiles successfully but when executed produces a simple "segmentation fault" message. The problem here is the fink-installed compilers. Harry Powell and Daniel O'Donovan have guided me to the light - the High Performance Computing for Mac OS X webpage (http://hpc.sourceforge.net) has binaries for the gcc 4.5 compiler package, which installs in /usr/local/. Compilation with this compiler set produces a working CNS executable. The only other modification is to copy the Makefile.header.2.gfortran file from cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux to cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux. Compile with 'make install compiler=gfortran', making sure that /usr/local/path is in $PATH. With the Intel 11.1 compilers (and I used the evaluation version here), CNS compiles successfully, but fails on execution. Thanks to Axel Brunger and Benjamin Bardiaux, for sharing that the Intel fortran compiler is not compatible with Xcode 3.2.2, although it does not seem to break gfortran in this case. A little more information can be found here: http://software.intel.com/en-us/articles/intel-fortran-for-mac-os-x-incompatible-with-xcode-322/ Thanks goes to Benjamin Bardiaux for the link. The webpage suggests two fixes. One is to add the '-use-asm' option to both the compilation and linker lines. This seems to work, and produces a working CNS executable. Not until now did I consider Xcode to be the problem, and at no point over the past few days did I come across or register the intel webpage linked above during my hours of google-trawling. The other option is to reinstall Xcode 3.2.1, which I assume is the version Axel Brunger said he reinstalled. This can be downloaded from the Mac Development Centre. Then reinstall the Intel fortran compiler. I have not tried this option, since the first option seems to have worked quite well. Thanks once again, Pryank On 9 Jun 2010, at 19:54, Axel Brunger wrote: Please note that the latest version of Xcode in Mac OS X 10.6.3 breaks the Intel Fortran and C compilers. It is possible that Xcode also breaks gfortran, but I haven't tested it. I've reverted to the Xcode version that came with the original Snow Leopard release. Intel is aware of the problem, but so far there have been no updates of the Intel compilers to fix the problem with Xcode. Axel Brunger On Jun 9, 2010, at 11:35 AM, Ethan Merritt wrote: On Wednesday 09 June 2010 10:45:07 am James Holton wrote: I have often wondered how it is that one can actually run and play games like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of the EPROM cartridges that I used to put into my Atari 2600 (circa 1982), but for some reason programs written just a few years ago will neither compile nor run on the "latest and greatest" linux/gcc systems. I seriously doubt that your Atari PacMan program was written in Fortran! But more to the point, to run it now you run an emulator for the original Atari chipset. PacMac runs around thinking he really is on an Atari console, blissfully unaware that the console is only an emulated simulation of the original long-gone world. Welcome to the matrix. Am I missing something? I think you are missing the mark twice in mentioning "linux/gcc". The complaint under discussion is with OSX, not a linux system. With rare exceptions, old linux programs run just fine on an up-to-date linux system, so long as you also install equally old versions of the support libraries. Do you have a counter-example in mind? In the specific case of old Fortran programs, the reality is that in the era of commercial Fortran compilers there was great divergence in the details of the implementation, particular with regard to I/O commands. gcc/f77/g77 was never a good Fortran compiler, and was particularly bad at compiling code idioms used by "real-world" Fortran code written for compilers supported by IBM, DEC, CDC, etc. gfortran is somewhat better, but still far from perfect. As to Pryank's problem: Pryank Patel wrote: Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on other lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no success so far. I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version 10.3.0) and am unable to compile cns v1.21 from source, using either the gcc 4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1 (evaluation) compilers. I may be mis-remembering, but I have it in mind that the cns source code requires selecting or porting a set of compiler-specific routines in one of the source modules. These are work-arounds for the variability in Fortran implementations mentioned above. Did you tweak this file appropriately for each of the compilers you tried? As a practical matter, you might want to look into running a VMWare layer on your machine so that you can compile and run linux executables rather than fighting the native OSX environment. You too can join PacMac in the happy world recreated in the matrix :-) Ethan I am aware that there are Mac OSX binaries available, but I am also using CNS for NMR structure calculation with the Aria 2.3 program, and to run that successfully CNS needs to be re-compiled with Aria-specific source code. With the gcc4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. When I try to execute cns, either with './cns' or by running one of the test scripts, I get the following: dmemory error code = ****** %ALLHP error encountered: fatal coding error (CNS is in mode: SET ABORT=NORMal END) ***************************************************** ABORT mode will terminate program execution. ***************************************************** Program will stop immediately. ============================================================ Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 8 bytes Program started at: on Program stopped at: 14:32:05 on 07-Jun-2010 CPU time used: 0.0036 seconds ============================================================ With 4.2.1 (using gfortran), CNS fails at the linking stage with "Undefined symbols:" errors. With 4.4, CNS compiles successfully, but when executed produces a simple "segmentation fault" message. With the 11.1 Intel compilers, CNS compiles successfully, but fails on execution: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source cns 000000010029C7BE _xtarmoin_ 1813 xdeclare.f cns 000000010029C68E _xreres_ 764 xdeclare.f cns 000000010003E04A _MAIN__ 167 cns.f cns 000000010000184C Unknown Unknown Unknown cns 00000001000017E4 Unknown Unknown Unknown I have checked my shell stack limit, and to make sure, I set the shell stacksize using "ulimit -s 65532" (which I believe is the upper limit on Mac OSX) and by using the ifort linker option. Both of which made no difference. I then added some compiler options in an attempt to obtain more debugging information, including "-check bounds -g" and "-heap-arrays". The following occurs on execution: forrtl: severe (408): fort: (2): Subscript #1 of the array HEAP has value 155357288 which is greater than the up per bound of 15 Image PC Routine Line Source cns 000000010087410C Unknown Unknown Unknown cns 0000000100872C44 Unknown Unknown Unknown cns 000000010082BCCE Unknown Unknown Unknown cns 00000001007E36AA Unknown Unknown Unknown cns 00000001007E3AF7 Unknown Unknown Unknown cns 00000001002B48A4 _allhp_ 326 heap.f cns 00000001002B7EC6 _heapvfy_ 93 heapvfy.f cns 0000000100071409 _MAIN__ 60 cns.f cns 0000000100000D5C Unknown Unknown Unknown cns 0000000100000CF4 Unknown Unknown Unknown Any help/ideas would be very much appreciated. Best wishes, Pryank -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web: http://atbweb.stanford.edu<http://atbweb.stanford.edu/> Email: brun...@stanford.edu<mailto:brun...@stanford.edu> Phone: +1 650-736-1031 Fax: +1 650-745-1463
