Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#38820 closed defect (fixed)

port atlas fails to upgrade

Reported by: aranoya@… Owned by: Veence (Vincent)
Priority: Normal Milestone:
Component: ports Version: 2.1.3
Keywords: Cc: cooljeanius (Eric Gallager), McBeath@…, aranoya@…
Port: atlas

Description (last modified by mf2k (Frank Schima))

i got the following error while upgrading atlas

----
sudo port upgrade atlas
--->  Computing dependencies for atlas
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets

main.log is attached.

thanks

Attachments (4)

main.log (176.2 KB) - added by aranoya@… 12 years ago.
log file
main.2.log (4.3 MB) - added by McBeath@… 12 years ago.
Crash after r105312 was used
main.3.log (4.3 MB) - added by aranoya@… 12 years ago.
crash after new port file
main.4.log (26.4 KB) - added by atif.azad@… 12 years ago.
Main.log

Change History (32)

Changed 12 years ago by aranoya@…

Attachment: main.log added

log file

comment:1 Changed 12 years ago by aranoya@…

Cc: aranoya@… added

vince@…

Last edited 12 years ago by aranoya@… (previous) (diff)

comment:2 Changed 12 years ago by mf2k (Frank Schima)

Cc: aranoya@… removed
Description: modified (diff)
Owner: changed from macports-tickets@… to vince@…

In the future, please use WikiFormatting.

comment:3 Changed 12 years ago by cecilyen@…

Cc: cecilyen@… added

Cc Me!

comment:4 Changed 12 years ago by Veence (Vincent)

This is a clear bug in clang/llvm-3.3. Try again with the new Portfile (r105312). If you still get the same error, you should report it to the clang/llvm developers.

comment:5 Changed 12 years ago by Veence (Vincent)

I’ve disabled the vectorizing flags for clang3.3 in r105324. Please retry (everyone).

comment:6 Changed 12 years ago by Veence (Vincent)

This is definitely a regression in clang. With clang-mp-3.3 r173279, compilation is fine:

/opt/local/bin/clang-mp-3.3 -c -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei2 -DATL_CPUMHZ=2300 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2300 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -fvectorize -fslp-vectorize -march=native -mavx  /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//tune/blas/gemm/gmmsearch.c
In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//tune/blas/gemm/gmmsearch.c:34:
In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmtesttime.h:4:
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmparse.h:1011:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
   while (ln = GetJoinedLines(fpin))
          ~~~^~~~~~~~~~~~~~~~~~~~~~
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmparse.h:1011:14: note: place parentheses around the assignment to silence this warning
   while (ln = GetJoinedLines(fpin))
             ^
          (                        )
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/atlas_mmparse.h:1011:14: note: use '==' to turn this assignment into an equality comparison
   while (ln = GetJoinedLines(fpin))
             ^
             ==
1 warning generated.
/opt/local/bin/clang-mp-3.3 -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.10.1/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei2 -DATL_CPUMHZ=2300 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2300 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -fvectorize -fslp-vectorize -march=native -mavx  -o xgmmsearch gmmsearch.o
./xgmmsearch -p s -r -1

Last edited 12 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:7 Changed 12 years ago by cooljeanius (Eric Gallager)

Cc: egall@… added

Cc Me!

Changed 12 years ago by McBeath@…

Attachment: main.2.log added

Crash after r105312 was used

comment:8 Changed 12 years ago by McBeath@…

Thanks for the patch. The first compile issue was fixed, but the regression fought back. There seems to be a -vectorize-loops which kills the build at a later stage. Please find attached the main.log

clang/llvm seems to be really broken

Last edited 12 years ago by McBeath@… (previous) (diff)

comment:9 Changed 12 years ago by Veence (Vincent)

Indeed, and there is not much left to do, except banning the use of clang until these bigs are fixed…

Sigh…

comment:10 Changed 12 years ago by McBeath@…

Cc: McBeath@… added

Cc Me!

comment:11 Changed 12 years ago by aranoya@…

Thanks for the patch. As commented above, it now fails at a later stage. Main.log is attached.

Thanks

Changed 12 years ago by aranoya@…

Attachment: main.3.log added

crash after new port file

comment:12 Changed 12 years ago by aranoya@…

Cc: aranoya@… added

Cc Me!

comment:13 Changed 12 years ago by Veence (Vincent)

r105342 should disable clang as a possible compiler and reverts default choice to gcc47 for all machines. Please test and tell me.

comment:14 Changed 12 years ago by Veence (Vincent)

PS: I really encourage you to report the clang bugs you found upstream. It is the only way to eventually get a version that will work and support AVX kernels (performace x2 w/r SSE).

comment:15 in reply to:  13 Changed 12 years ago by dhuffkc@…

Replying to vince@…:

r105342 should disable clang as a possible compiler and reverts default choice to gcc47 for all machines. Please test and tell me.

Works for me...thanks!

--Don

comment:16 Changed 12 years ago by Veence (Vincent)

Resolution: fixed
Status: newclosed

Thanks. I’m going to commit a final patch and rev-bump the Portfile. I close this bug series. If anyone still experiences a problem, please reopen it.

r105428

comment:17 in reply to:  16 Changed 12 years ago by aranoya@…

Replying to vince@…:

Thanks. I’m going to commit a final patch and rev-bump the Portfile. I close this bug series. If anyone still experiences a problem, please reopen it.

r105428

Thanks a lot, it worked for me as well.

comment:18 Changed 12 years ago by Veence (Vincent)

Following r105491 that upgrades clang-3.3, I have re-enabled the +clang33 variant, but I have not bumped the revision yet. Please update, test and report any error you might find, especially on AVX (Core i2 +) machines.

Thanks !

comment:19 in reply to:  4 Changed 12 years ago by atif.azad@…

Replying to vince@…:

This is a clear bug in clang/llvm-3.3. Try again with the new Portfile (r105312). If you still get the same error, you should report it to the clang/llvm developers.

I am also getting this error despite having the new file reported in that (r105312)

comment:20 Changed 12 years ago by atif.azad@…

I have made the changes as per https://trac.macports.org/changeset/105342

However when I do "sudo port upgrade installed", I still get the same error message :

Selected C compiler: /opt/local/bin/gcc-mp-4.7 Selected F77 compiler: gfortran47 ---> Building atlas Error: org.macports.build for port atlas returned: command execution failed Please see the log file for port atlas for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_math_atlas/atlas/main.log

Error: Unable to upgrade port: 1

comment:21 Changed 12 years ago by atif.azad@…

Resolution: fixed
Status: closedreopened

comment:22 in reply to:  20 Changed 12 years ago by mf2k (Frank Schima)

Replying to atif.azad@…:

I have made the changes as per https://trac.macports.org/changeset/105342

What do you mean? Hopefully you simply ran.

sudo port selfupdate

However when I do "sudo port upgrade installed",

You should normally not upgrade all installed ports. You probably want to then run:

sudo port upgrade outdated

comment:23 Changed 12 years ago by mf2k (Frank Schima)

Resolution: fixed
Status: reopenedclosed

Please don't re-open a fixed ticket without attaching a main.log.

Also, please use WikiFormatting in your comments.

comment:24 in reply to:  20 ; Changed 12 years ago by Veence (Vincent)

Replying to atif.azad@…:

I have made the changes as per https://trac.macports.org/changeset/105342

However when I do "sudo port upgrade installed", I still get the same error message :

Selected C compiler: /opt/local/bin/gcc-mp-4.7 Selected F77 compiler: gfortran47

This ticket was about Atlas and Clang. It appears you use gcc47 to compile Atlas, so your issue is unrelated to this ticket. Please file a new bug and attach the log file if your problem persist.

Changed 12 years ago by atif.azad@…

Attachment: main.4.log added

Main.log

comment:25 Changed 12 years ago by atif.azad@…

Please note that I am behind a proxy so had to run:

sudo port -d sync and now ran

sudo port upgrade outdated

Above I have attached the Main.log

comment:26 in reply to:  25 Changed 12 years ago by larryv (Lawrence Velázquez)

You didn’t clean atlas, so this main.log is not useful. Please run sudo port clean atlas, open a new ticket, and attach the log there. This ticket does not apply to you.

comment:27 in reply to:  24 Changed 12 years ago by larryv (Lawrence Velázquez)

Replying to vince@…:

This ticket was about Atlas and Clang. It appears you use gcc47 to compile Atlas, so your issue is unrelated to this ticket. Please file a new bug and attach the log file if your problem persist.

The new ticket is #39065, I think.

comment:28 Changed 12 years ago by cecilyen@…

Cc: cecilyen@… removed

Cc Me!

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