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#6 Errors building on cygwin

closed-fixed
None
5
2015-03-21
2009-09-29
John McDonald
No

I am trying to build ATLAS on a Intel Core 2 T7600 machine using cygwin and visual studio 2005. I am completely new to ATLAS (and so could be doing something stupid here!).

I have downloaded ATLAS3.9.14.tar.bz2 and unpacked it to c:\ATLAS3.9.14.
I created a subdirectory called Vista.
I have gone through the errata and added the references to vs2005 for cygwin.bat.

My problem I can't get the configure script to run successfully. Below is a cut-and-paste of the output that is generated from attempting both -b 32 and -b64. I would appreciate any guidance anyone can give me on this. If I can provide extra information please let me know.

I have tried to generate an error report, again without success. To do this I cd into the top-level directory and run "make error_report arch=" but this returns a "No rule to make target..." error.

Thanks,

John McDonald.

$ ../configure -b 32 -D c -DPentiumCPS=2330 -C ic cl
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -c /cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/atlconf_mi
sc.c
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -o xconfig /cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/co
nfig.c atlconf_misc.o
./xconfig -d s /cygdrive/c/ATLAS3.9.14/Vista/../ -d b /cygdrive/c/ATLAS3.9.14/Vista -b 32 -D c -DPentiumCPS=2330 -C ic
cl

OS configured as WinNT (8)

Assembly configured as GAS_x8632 (1)
0 [main] xprobe_3dnow 229688 _cygtls::handle_exceptions: Error while dumping state (probably corrupted stack)

Vector ISA Extension configured as SSE3 (2,28)

Architecture configured as Core2 (15)

Clock rate configured as 14Mhz

Maximum number of threads configured as 2
Parallel make command configured as '$(MAKE)'
Cannot detect CPU throttling.
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -c /cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/probe_comp
.c
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -o xprobe_comp probe_comp.o atlconf_misc.o
rm -f config1.out
make atlas_run atldir=/cygdrive/c/ATLAS3.9.14/Vista exe=xprobe_comp args="-v 0 -o atlconf.txt -O 8 -A 15 -Si nof77 0 -C
ic 'cl' -b 32" \ redir=config1.out
make[1]: Entering directory `/cygdrive/c/ATLAS3.9.14/Vista'
cd /cygdrive/c/ATLAS3.9.14/Vista ; ./xprobe_comp -v 0 -o atlconf.txt -O 8 -A 15 -Si nof77 0 -C ic 'cl' -b 32 > config1
.out
gcc: The -mno-cygwin flag has been removed; use a mingw-targeted cross-compiler.

make[2]: *** [/usr/local/bin/ATLwin_cl.exe] Error 1
Unable to to build ATLwin_cl, quitting
cmnd='make wind=/usr/local/bin /usr/local/bin/ATLwin_cl.exe
'
make[1]: *** [atlas_run] Error 255
make[1]: Leaving directory `/cygdrive/c/ATLAS3.9.14/Vista'
make: *** [IRun_comp] Error 2
assertion "!system(ln)" failed: file "/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/config.c", line 125
9 [sig] xconfig 229340 _cygtls::handle_exceptions: Error while dumping state (probably corrupted stack)
/bin/sh: line 1: 229340 Segmentation fault (core dumped) ./xconfig -d s /cygdrive/c/ATLAS3.9.14/Vista/../ -d b /cyg
drive/c/ATLAS3.9.14/Vista -b 32 -D c -DPentiumCPS=2330 -C ic cl
xconfig exited with 139

john@johnmcd-xps /cygdrive/c/ATLAS3.9.14/Vista
$ rm -rf *

$ ../configure -b 64 -D c -DPentiumCPS=2330 -C ic cl
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -c /cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/atlconf_mi
sc.c
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -o xconfig /cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/co
nfig.c atlconf_misc.o
./xconfig -d s /cygdrive/c/ATLAS3.9.14/Vista/../ -d b /cygdrive/c/ATLAS3.9.14/Vista -b 64 -D c -DPentiumCPS=2330 -C ic
cl

OS configured as WinNT (8)

Assembly configured as GAS_x8632 (1)
0 [main] xprobe_3dnow 233688 _cygtls::handle_exceptions: Error while dumping state (probably corrupted stack)

Vector ISA Extension configured as SSE3 (2,28)

Architecture configured as Core2 (15)

Clock rate configured as 14Mhz

Maximum number of threads configured as 2
Parallel make command configured as '$(MAKE)'
Cannot detect CPU throttling.
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -c /cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/probe_comp
.c
gcc -I/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/include -g -w -o xprobe_comp probe_comp.o atlconf_misc.o
rm -f config1.out
make atlas_run atldir=/cygdrive/c/ATLAS3.9.14/Vista exe=xprobe_comp args="-v 0 -o atlconf.txt -O 8 -A 15 -Si nof77 0 -C
ic 'cl' -b 64" \ redir=config1.out
make[1]: Entering directory `/cygdrive/c/ATLAS3.9.14/Vista'
cd /cygdrive/c/ATLAS3.9.14/Vista ; ./xprobe_comp -v 0 -o atlconf.txt -O 8 -A 15 -Si nof77 0 -C ic 'cl' -b 64 > config1
.out
gcc: The -mno-cygwin flag has been removed; use a mingw-targeted cross-compiler.

make[2]: *** [/usr/local/bin/ATLwin_cl.exe] Error 1
Unable to to build ATLwin_cl, quitting
cmnd='make wind=/usr/local/bin /usr/local/bin/ATLwin_cl.exe
'
make[1]: *** [atlas_run] Error 255
make[1]: Leaving directory `/cygdrive/c/ATLAS3.9.14/Vista'
make: *** [IRun_comp] Error 2
assertion "!system(ln)" failed: file "/cygdrive/c/ATLAS3.9.14/Vista/..//CONFIG/src/config.c", line 125
9 [sig] xconfig 234480 _cygtls::handle_exceptions: Error while dumping state (probably corrupted stack)
/bin/sh: line 1: 234480 Segmentation fault (core dumped) ./xconfig -d s /cygdrive/c/ATLAS3.9.14/Vista/../ -d b /cyg
drive/c/ATLAS3.9.14/Vista -b 64 -D c -DPentiumCPS=2330 -C ic cl
xconfig exited with 139

Discussion

  • One thing to scope out is that cygwin's gcc appears to have a compiler error:
    https://sourceforge.net/tracker/?func=detail&aid=2873570&group_id=23725&atid=379483

    I will have to try a mixed MSVC++ install as soon as I can get the required software installed. In the meantime, can you try a configure w/o the -C ic flag after doing applying the above compiler error workaround? If we can't get an all-gnu install to work, there is no point trying to get a mixed compiler install!

    Thanks,
    Clint

     
    • milestone: --> 148063
    • assigned_to: nobody --> rwhaley
     
    • labels: 320139 -->
    • milestone: 148063 -->
     
  • Hi,

    I am very sorry for the looong delay, but I think I have gotten Windows fully supported in ATLAS 3.9.79. Using it, you can build 32-bit libs using either the cygwin compilers or the MinGW compilers, though you still need cygwin installed. The ATLAS installation guide that comes with the tarfile has Windows-specific installation instructions.

    Can you try 3.9.79 and let me know if it works for you?

    Many thanks,
    Clint

     
    • status: open --> closed-fixed