Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Dear Fred, I would say that you're using a buggy gfortran version (http://lists.debian.org/debian-gcc/2009/03/msg00070.html). You may want to check your version with 'gfortran --version' in order to be sure of it. The '-malign-double' switch provides only a slight optimization and as you have already proven, it may be removed with very little impact on performance. Cheers, Jon 2013/3/6 vellieux frederic.velli...@ibs.fr: Dear all, By popular request here is an example of some code where gfortran gives run time errors. This is at the very beginning of the program, the first write statement where a parenthesis is seen as missing at run time: (the first hyphens are not within the Fortran code but there to indicate the number of spaces before each character, 6 and nothing more or less). Also enclosed as part.f herewith (as an attachment) [I must admit that, somehow, when modifying a Fortran program using vim on this new box, the number of characters at the beginning of Fortran cards seems to reset to 8 when there are 6 blanks to start with, I have no idea why this is so.] Help most welcome, and I'd hate to have to retype every single program... Ta, Fred. -- ORDER='A' NATM=0 DO 5,I=1,3 NGRID(2,I)= 9 NGRID(3,I)=-9 XMIN(I)= . XMAX(I)=-. 5 CONTINUE C C OPEN INPUT FILE C WRITE (*,10) 10 FORMAT(///,25X,'*', . /,25X,'* *', -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi Jon, Thanks for the feedback. The version I am using (which is not that reported in the web page you mention, Version: 4:4.3.2-2) is: GNU Fortran (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4). Hence it appears that the bug hasn't been entirely dealt with. Ian Tickle was getting segmentation faults (so he may be using gfortran V 4.3.2-2), I was only getting a binary that crashes due to a missing left parenthesis in a FORMAT statement (the parenthesis was there as far as I could see...). Thanks again, Fred. On 07/03/13 10:23, Jon Agirre wrote: Dear Fred, I would say that you're using a buggy gfortran version (http://lists.debian.org/debian-gcc/2009/03/msg00070.html). You may want to check your version with 'gfortran --version' in order to be sure of it. The '-malign-double' switch provides only a slight optimization and as you have already proven, it may be removed with very little impact on performance. Cheers, Jon -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
I'm using gcc 4.7.2 (latest stable version I think). I don't get the compilation error of the FORMAT statement but I do get the segfault error on running with the '-malign-double' switch that I reported. So it would appear that even the current stable version is buggy! As Jon said the workaround is to leave off '-malign-double': it has very little effect on performance anyway. Or use ifort (main reason I use it is past bugs in Gnu compilers). Cheers -- Ian On 7 March 2013 09:44, vellieux frederic.velli...@ibs.fr wrote: Hi Jon, Thanks for the feedback. The version I am using (which is not that reported in the web page you mention, Version: 4:4.3.2-2) is: GNU Fortran (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4). Hence it appears that the bug hasn't been entirely dealt with. Ian Tickle was getting segmentation faults (so he may be using gfortran V 4.3.2-2), I was only getting a binary that crashes due to a missing left parenthesis in a FORMAT statement (the parenthesis was there as far as I could see...). Thanks again, Fred. On 07/03/13 10:23, Jon Agirre wrote: Dear Fred, I would say that you're using a buggy gfortran version (http://lists.debian.org/**debian-gcc/2009/03/msg00070.**htmlhttp://lists.debian.org/debian-gcc/2009/03/msg00070.html). You may want to check your version with 'gfortran --version' in order to be sure of it. The '-malign-double' switch provides only a slight optimization and as you have already proven, it may be removed with very little impact on performance. Cheers, Jon -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
[ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi Fred If you look very carefully at your Fortran code you will probably find a small error/inconsistency that g77 allowed but gfortran picked up on or compiled as written rather than as intended. My move from g77 to gfortran when building Mosflm (which is moderately large) was pretty painless, but I did find that when I got errors of this type the fault was when the code did not adhere to standards. Generally speaking, gfortran adheres to the current Fortran standards more strictly than g77. Recent versions give Mosflm executables that are within a few percent of the performance that I get with the Intel Fortran ifort compilers (actually, sometimes faster, sometimes slower)- I've checked this on both Mac and Linux. I use gfortran for development, ifort for checking things are still okay, and also run an old Linux box with g77 for further checking in case I've missed something earlier. My Windows executable of Mosflm still uses g77 (the mingw cross-compiler run on OSX). However, there are persistent reports out there of people who find their code runs much faster when compiled with ifort - so I guess this is very much code dependent. I can have a look at your code if it would help. HTH On 6 Mar 2013, at Wed6 Mar 09:48, vellieux wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign- double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi Fred I regularly compile F77 code with gfortran: I always get lots of warnings and the occasional error that I didn't get with g77 mainly because gfortran is much stricter applying the standard (and a good thing too!). I also regularly use ifort (which isn't quite as strict as gfortran and consequently sometimes doesn't spot some real errors). Maybe if you could post the bit of code it's complaining about (including say +=5 lines on each side) we could make some specific suggestions. It's hard to make suggestions which will cover all eventualities. Cheers -- Ian On 6 March 2013 09:48, vellieux frederic.velli...@ibs.fr wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi Fred, From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of vellieux [frederic.velli...@ibs.fr] When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format It might be something to do with fixed vs free format, although I'd have thought the -std=legacy should have dealt with that. You could try adding -ffixed-format and maybe experiment with different values for -ffixed-line-length Things that have bitten me in the past include different backslash interpretations, so you could try -fbackslash and also -fd-lines-as-comments if there are lines beginning with a D. If none of that works, maybe you could post the bit of code around the lines where you're seeing the error message to see if someone can spot what's tripping the compiler up. Best wishes, Jens
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi Fred, vellieux frederic.velli...@ibs.fr writes: [...] I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format [...] Mmm, that kind of error rings a bell … is the relevant format a string rather than given in a FORMAT statement? If so, you need round brackets INSIDE the format string, i.e. write (*, '(i5)') 123 rather than write (*, 'i5') 123 —this can manifest itself at run‐time, especially if the format is in a character variable. -- Ian ◎
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Dear all, By popular request here is an example of some code where gfortran gives run time errors. This is at the very beginning of the program, the first write statement where a parenthesis is seen as missing at run time: (the first hyphens are not within the Fortran code but there to indicate the number of spaces before each character, 6 and nothing more or less). Also enclosed as part.f herewith (as an attachment) [I must admit that, somehow, when modifying a Fortran program using vim on this new box, the number of characters at the beginning of Fortran cards seems to reset to 8 when there are 6 blanks to start with, I have no idea why this is so.] Help most welcome, and I'd hate to have to retype every single program... Ta, Fred. -- ORDER='A' NATM=0 DO 5,I=1,3 NGRID(2,I)= 9 NGRID(3,I)=-9 XMIN(I)= . XMAX(I)=-. 5 CONTINUE C C OPEN INPUT FILE C WRITE (*,10) 10 FORMAT(///,25X,'*', . /,25X,'* *', -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 ORDER='A' NATM=0 DO 5,I=1,3 NGRID(2,I)= 9 NGRID(3,I)=-9 XMIN(I)= . XMAX(I)=-. 5 CONTINUE C C OPEN INPUT FILE C WRITE (*,10) 10 FORMAT(///,25X,'*', . /,25X,'* *',
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Fred The relevant bit of code, with the FORMAT statement closed with a ')' and an END statement added to make it a viable program, is: WRITE (*,10) 10 FORMAT(///,25X,'*', . /,25X,'* *') END For me this compiles and runs without error using gfortran (gcc version 4.7.2). Maybe you have an old version of gfortran with bugs. Note that a statement with continuation lines containing errors usually generates an error message which specifies only the first line of the statement. What's in the rest of the FORMAT statement? -- Ian On 6 March 2013 10:37, vellieux frederic.velli...@ibs.fr wrote: Dear all, By popular request here is an example of some code where gfortran gives run time errors. This is at the very beginning of the program, the first write statement where a parenthesis is seen as missing at run time: (the first hyphens are not within the Fortran code but there to indicate the number of spaces before each character, 6 and nothing more or less). Also enclosed as part.f herewith (as an attachment) [I must admit that, somehow, when modifying a Fortran program using vim on this new box, the number of characters at the beginning of Fortran cards seems to reset to 8 when there are 6 blanks to start with, I have no idea why this is so.] Help most welcome, and I'd hate to have to retype every single program... Ta, Fred. -- ORDER='A' NATM=0 DO 5,I=1,3 NGRID(2,I)= 9 NGRID(3,I)=-9 XMIN(I)= . XMAX(I)=-. 5 CONTINUE C C OPEN INPUT FILE C WRITE (*,10) 10 FORMAT(///,25X,'***', . /,25X,'* *', -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi all, Problem solved thanks to Jorge Navaza's suggestion: remove all compilation flags but only have -Wall as a compilation flag. There is no run time error any more and there is no error at compilation time. The program runs fine. Thanks to Thomas Jens, Harry Powell, Ian Tickle, Ian Clifton and Bernhard Rupp for their suggestions. Fred. On 06/03/13 10:48, vellieux wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Fred, OK I just noticed I didn't have the -malign-double flag. With that it compiles but on running I get: Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x12244B #1 0x122A9C #2 0x473907 #3 0x1BD238 #4 0x1CB4BF #5 0x80486E2 in MAIN__ Segmentation fault Without that flag it compiles runs without error. So you may want to try it just without that flag. Cheers -- Ian On 6 March 2013 12:33, vellieux frederic.velli...@ibs.fr wrote: Hi all, Problem solved thanks to Jorge Navaza's suggestion: remove all compilation flags but only have -Wall as a compilation flag. There is no run time error any more and there is no error at compilation time. The program runs fine. Thanks to Thomas Jens, Harry Powell, Ian Tickle, Ian Clifton and Bernhard Rupp for their suggestions. Fred. On 06/03/13 10:48, vellieux wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi again Ian and list, The following flags seem to work fine: gfortran -o ../bin/$1 -std=legacy -ffixed-format -Wno-globals -w -O3 -funroll-loops -ffast-math -fno-second-underscore $1.f (followed by the library or libraries, compiled with the same flags). Problem solved as far as I am concerned (until there is yet another compiler I guess, next Linux box down the road). Fred. On 06/03/13 13:55, Ian Tickle wrote: Fred, OK I just noticed I didn't have the -malign-double flag. With that it compiles but on running I get: Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x12244B #1 0x122A9C #2 0x473907 #3 0x1BD238 #4 0x1CB4BF #5 0x80486E2 in MAIN__ Segmentation fault Without that flag it compiles runs without error. So you may want to try it just without that flag. Cheers -- Ian -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)
Hi, The command: $ aptitude install fort77 would install an f77 command on Ubuntu/Debian Linux. In fact that's a wrapper for f2c, but maybe it behaves like a real f77 compiler, I would give it a try personnally. On 03/06/2013 06:48 PM, vellieux wrote: Hello, For those who still know the Fortran language and its Fortran 77 variant, I used to have a g77 compiler here (Linux box), and now on the new box it's no longer g77 but gfortran. When compiling Fortran77 code (these are the flags used for compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the libraries on that same compile line) I get errors (at run time) of the type: At line 138 of file program.f (unit = 6, file = 'stdout') Fortran runtime error: Missing initial left parenthesis in format When looking at this code (which compiled perfectly well using g77 - I removed the flag -fno-globals which doesn't seem to exist any more in gfortran) the Fortran code that I see appears to have all parentheses in the correct places. Any idea of what must be done with existing Fortran 77 code in order to get it to compile and run with gfortran ? Otherwise any idea which compiler should be used to compile Fortran 77 code ? Thanks in advance, Fred.
