Crystallography Online: the website of the International Union of Crystallography

Dear Jon,

   I have most of what is needed for g95 ready to go, but there
is one puzzling problem left -- when working with the 3d array
test cases, as in your report, I am getting what seems to be
misindexing for 40,40,50 and up in an array that is 50x60x70.
The 2d cases work like a champ, and the 3d test works up to that
point.  Any compiler option suggestions before I revert to manual
indexing?

   Regards,
     Herbert

P.S.  I had to change your fix to fcb_read_bits.m4 to keep it
working with gfortran as well as g95.  Here is the updated patch:

*** fcb_read_bits.m4      Sun Apr  1 22:12:49 2007
--- fcb_read_bits.m4    Mon May  7 20:28:57 2007
***************
*** 17,23 ****
         INTEGER,      INTENT(IN):: LINT
         INTEGER(4),  INTENT(OUT):: IINT(LINT)
         INTEGER                    I,J,LBITCOUNT,COUNT,KINTS
!       INTEGER(8)                 BITCODE,TBITCODE, M
   !-----------------------------------------------------------------------

         INTEGER                    MAXBITS, NUMINTS
--- 17,23 ----
         INTEGER,      INTENT(IN):: LINT
         INTEGER(4),  INTENT(OUT):: IINT(LINT)
         INTEGER                    I,J,LBITCOUNT,COUNT,KINTS
!       INTEGER(8)                 BITCODE,TBITCODE, M, MASK8
   !-----------------------------------------------------------------------

         INTEGER                    MAXBITS, NUMINTS
***************
*** 26,37 ****
   `
         MAXBITS = 32
         NUMINTS = (BITCOUNT+MAXBITS-1)/MAXBITS
        
         DO KINTS = 1,NUMINTS
           LBITCOUNT = MAXBITS
           IF (KINTS.EQ.NUMINTS) LBITCOUNT = BITCOUNT-(NUMINTS-1)*32
           COUNT = BCOUNT
!         BITCODE = IAND(BBYTE,Z''`000000FF''`)
           DO
             IF (COUNT .GE. LBITCOUNT) EXIT
             BYTE_IN_FILE=BYTE_IN_FILE+1
--- 26,39 ----
   `
         MAXBITS = 32
         NUMINTS = (BITCOUNT+MAXBITS-1)/MAXBITS
+       MASK8 = Z''`000000FF''`
        
         DO KINTS = 1,NUMINTS
           LBITCOUNT = MAXBITS
           IF (KINTS.EQ.NUMINTS) LBITCOUNT = BITCOUNT-(NUMINTS-1)*32
           COUNT = BCOUNT
!         BITCODE = BBYTE
!         BITCODE = IAND(BITCODE,MASK8)
           DO
             IF (COUNT .GE. LBITCOUNT) EXIT
             BYTE_IN_FILE=BYTE_IN_FILE+1
***************
*** 40,46 ****
               REC_IN_FILE,BYTE_IN_FILE,BBYTE)
             IF (FCB_READ_BITS.NE.0) RETURN
               BCOUNT=8
!             TBITCODE = IAND(BBYTE,Z''`000000FF''`)
               CALL MVBITS(TBITCODE,0,MIN(8,32-COUNT),BITCODE,COUNT)
               COUNT = COUNT+8
           END DO
--- 42,49 ----
               REC_IN_FILE,BYTE_IN_FILE,BBYTE)
             IF (FCB_READ_BITS.NE.0) RETURN
               BCOUNT=8
!             TBITCODE = BBYTE
!             TBITCODE = IAND(TBITCODE,MASK8)
               CALL MVBITS(TBITCODE,0,MIN(8,32-COUNT),BITCODE,COUNT)
               COUNT = COUNT+8
           END DO
***************
*** 62,68 ****
           ! SAVE THE REMAINING BITS FOR NEXT TIME
        
           TBITCODE = BBYTE
!         TBITCODE = 
ISHFT(IAND(TBITCODE,Z''`000000FF''`),-(BCOUNT-(COUNT-LBITCOUNT)) )
           BBYTE = TBITCODE
           BCOUNT = COUNT-LBITCOUNT
        
--- 65,71 ----
           ! SAVE THE REMAINING BITS FOR NEXT TIME
        
           TBITCODE = BBYTE
!         TBITCODE = ISHFT(IAND(TBITCODE,MASK8),-(BCOUNT-(COUNT-LBITCOUNT)) )
           BBYTE = TBITCODE
           BCOUNT = COUNT-LBITCOUNT



At 1:09 PM -0400 5/7/07, Herbert J. Bernstein wrote:
>Dear Jon,
>
>   Thank you.  This is very helpful, and it is a good idea to send it
>to the list to save others from having to report the same problems.
>Since windows is a very odd case, I think I'll make a distinct
>Makefile_MINGW, rather than use a make.inc  I'll wait a couple of
>days for other trouble reports and put out an update with your
>changes early next week.
>
>   Regards,
>     Herbert
>
>At 6:29 PM +0200 5/7/07, Jon Wright wrote:
>>Dear Herbert,
>>
>>Here are some notes for compiling with the mingw system on windows. 
>>It is a free gnu c compiler with "msys" bash shell.  For f90 I used 
>>the g95 compiler ( www.g95.org ).
>>
>>g95 is fussy about the inline binary constants. A diff of 
>>fcb_read_bits.m4 should be attached - it could easily contain 
>>errors as I don't really know the intentions of the code. I have 
>>just used the transfer intrinsic to give a matching type to use in 
>>IAND.
>>
>>libmap.a is required for target 'all' in the Makefiles but my 
>>'make' doesn't see how to make it. I've attached an edited makefile 
>>for this compiler / platform. There are some issues with "time" not 
>>existing and, no directories /usr/bin etc. Might be worthwhile to 
>>have a Makefile and then a platform dependent make.inc ? I had to 
>>change in lots of places.
>>
>>My favourite windows C compiler (mingw gcc) didn't know about 
>>bzero: needed to add something near the top of cbf_codes.c:
>>
>>#ifdef __MINGW32__
>>#define bzero(ptr,size) memset (ptr, 0, size);
>>#endif
>>
>>
>>The needed to remove the -ansi flag from the makefile as "swab" 
>>function is otherwise hidden by an ifdef in <string.h>.
>>  src/cbf_uncompressed.c:431: warning: implicit declaration of function `swab'
>>
>>mkstemp is missing on mingw32 also (in img2cif.c etc), I have 
>>attached a header file implementation, but I am not sure if it 
>>works. If this is in the example directory then add this to 
>>img2cif.c, cif2cbf.c and convert_minicbf.c:
>>
>>#ifdef __MINGW32__
>>#include "mkstemp.h"
>>#endif
>>
>>It might be better to use tmpfile(?). /tmp exists on my system, but 
>>is extremely unlikely to be there in general. This change allows 
>>the programs to compile, but not pass the tests. It seems windows 
>>(mingw MSYS bash shell) does like reading or writing binary images 
>>through stdin or stdout. I changed the makefile to use filenames 
>>for the images. This means the mkstemp supplied may be no good. It 
>>might be better to force stdin and stdout to be binary streams in 
>>this case, as in 
>>(http://archives.postgresql.org/pgsql-hackers-win32/2005-01/msg00227.php)
>>
>>I can investigate further if you think it is likely that windows 
>>users will need this functionality.
>>
>>Since "time" is not a windows/dos command - I added a makefile 
>>variable $(TIME) which is empty for this system.
>>
>>Finally, I get a slew of test failures which make me worry I got 
>>the fortran wrong, trimmed output from "make tests" is attached. 
>>With the fixes it appears to be OK apart from the map part.
>>
>>I shall try to look at the python bindings again soon. Leaving 
>>tomorrow for the APS user meeting  for a week and then the UK for 
>>the week after.
>>
>>Best wishes,
>>
>>Jon
>>

-- 
=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya at dowling.edu
=====================================================