#38820 closed defect (fixed)
port atlas fails to upgrade
Reported by: | aranoya@… | Owned by: | Veence (Vincent) |
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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)
Change History (32)
Changed 12 years ago by aranoya@…
comment:2 Changed 12 years ago by mf2k (Frank Schima)
Cc: | aranoya@… removed |
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Description: | modified (diff) |
Owner: | changed from macports-tickets@… to vince@… |
In the future, please use WikiFormatting.
comment:4 follow-up: 19 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
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
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: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
comment:13 follow-up: 15 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 Changed 12 years ago by dhuffkc@…
comment:16 follow-up: 17 Changed 12 years ago by Veence (Vincent)
Resolution: | → fixed |
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Status: | new → closed |
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.
comment:17 Changed 12 years ago by aranoya@…
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 Changed 12 years ago by atif.azad@…
comment:20 follow-ups: 22 24 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 |
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Status: | closed → reopened |
comment:22 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 |
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Status: | reopened → closed |
Please don't re-open a fixed ticket without attaching a main.log.
Also, please use WikiFormatting in your comments.
comment:24 follow-up: 27 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.
comment:25 follow-up: 26 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 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.
log file