Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#10092 closed defect (fixed)

export FC, F77, F90 and F95 from scipy_sandbox

Reported by: David Kirkby Owned by: François Bissey
Priority: major Milestone: sage-4.6
Component: build Keywords:
Cc: Merged in:
Authors: David Kirkby Reviewers: François Bissey
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: Stopgaps:

Status badges

Description

scipy_sandbox is picking up the wrong Fortran compiler (Sun compiler in /usr/bin) and ignoring the contents of the file $SAGE_LOCAL/bin/sage_fortran This adds patch exports all 4 of these Fortran related variables, so scipy_sandbox uses the right compiler.

For reasons unknown, following the update of Numpy (#9808), it became necessary to export these Fortran variables on both SciPy and scipy_sandbox.

I also cleaned up SPKG.txt, as it was very bare.

Attachments (2)

10092-Resolve-Fortran-issues.patch (3.1 KB) - added by David Kirkby 12 years ago.
Export FC, F77, F90 and F95 variables so the right Fortran compiler is found.
10092-remove-Debian-stuff.patch (9.5 KB) - added by David Kirkby 12 years ago.
Remove Debian related file in accordance with #5903

Download all attachments as: .zip

Change History (24)

Changed 12 years ago by David Kirkby

Export FC, F77, F90 and F95 variables so the right Fortran compiler is found.

comment:1 Changed 12 years ago by David Kirkby

Status: newneeds_review

This is now ready for review. A package can be found at

http://boxen.math.washington.edu/home/kirkby/patches/scipy_sandbox-20071020.p6.spkg

Dave

comment:2 Changed 12 years ago by François Bissey

Status: needs_reviewpositive_review

It all look good to me. Bring it inline with the other packages and cannot possibly interfere with anything else. It's surprising it didn't need this earlier.

comment:3 Changed 12 years ago by François Bissey

Status: positive_reviewneeds_work

Oh no! This needs clean up as per #5903 (removal of debian stuff).

comment:4 Changed 12 years ago by David Kirkby

Give me 10 minutes and I'll remove the unneeded stuff.

dave

Changed 12 years ago by David Kirkby

Remove Debian related file in accordance with #5903

comment:5 Changed 12 years ago by David Kirkby

Status: needs_workneeds_review

comment:6 Changed 12 years ago by David Kirkby

I've deleted the Debian related files.

comment:8 Changed 12 years ago by François Bissey

Owner: changed from Georg S. Weber to François Bissey
Reviewers: François Bissey

patch looks fine, the spkg looks identical to the previous one. Unless I have a caching problem.

comment:9 in reply to:  8 Changed 12 years ago by David Kirkby

Replying to fbissey:

patch looks fine, the spkg looks identical to the previous one. Unless I have a caching problem.

I think you do have a caching problem. I just downloaded it myself with:

wget http://boxen.math.washington.edu/home/kirkby/patches/scipy_sandbox-20071020.p6.spkg

and it looks fine. The Debian stuff is removed from the .spkg.

drkirkby@hawk:/tmp/2/scipy_sandbox-20071020.p6$ ls -l
total 40
drwxr-xr-x   4 drkirkby staff        906 Dec  9  2007 arpack
drwxr-xr-x   3 drkirkby staff       1051 Feb  1  2008 delaunay
drwxr-xr-x   2 drkirkby staff        748 Dec  8  2007 patches
-rwxr-xr-x   1 drkirkby staff        831 Oct  7 00:12 spkg-install
-rw-r--r--   1 drkirkby staff       2279 Oct  7 23:23 SPKG.txt
drkirkby@hawk:/tmp/2/scipy_sandbox-20071020.p6$ 

Dave

comment:10 Changed 12 years ago by David Kirkby

The MD5 checksum of the package is e7df163ceb72d4f5aedbcab3ace90ebd

comment:11 Changed 12 years ago by François Bissey

Status: needs_reviewpositive_review

Just got it with wget instead of firefox and it looks fine now! Positive review it is then!

comment:12 in reply to:  11 Changed 12 years ago by David Kirkby

Replying to fbissey:

Just got it with wget instead of firefox and it looks fine now! Positive review it is then!

Thank you. I've been caught out with that before too.

Dave

comment:13 Changed 12 years ago by Mitesh Patel

Merged in: sage-4.6.alpha3
Resolution: fixed
Status: positive_reviewclosed

comment:14 Changed 12 years ago by David Kirkby

I note this failed to build on fulvia the Solaris x86 system. The buildbot log shows it failed

sage: An error occurred while installing scipy_sandbox-20071020.p6

though I can't see what anything other than the fact it failed. We might need to open a new ticket for this, or revert this change. I can't possibly understand how it can cause a problem on any platform, but it appears to have done on Solaris x86, which is especially strange given I tested this on OpenSolaris x86.

Dave

comment:15 in reply to:  14 Changed 12 years ago by François Bissey

Replying to drkirkby:

I note this failed to build on fulvia the Solaris x86 system. The buildbot log shows it failed

sage: An error occurred while installing scipy_sandbox-20071020.p6

though I can't see what anything other than the fact it failed. We might need to open a new ticket for this, or revert this change. I can't possibly understand how it can cause a problem on any platform, but it appears to have done on Solaris x86, which is especially strange given I tested this on OpenSolaris x86.

That's indeed very strange. Any chance that we will have access to a build log? CC me on any ticket you open about this please.

Francois

comment:16 Changed 12 years ago by Mitesh Patel

Here's the error message:

./spkg-install: FC=/home/buildbot/build/sage/fulvia-1/fulvia_full/build/sage-4.6.alpha3/local/bin/sage_fortran: is not an identifier

I think fulvia's /bin/sh does not support the compact export FOO=bar. Maybe we should just make spkg-install a bash script?

David or François, could one of you please open a 4.6 blocker to fix this?

By the way, adding links to individual spkg logs is already on the Sage Buildbot TODO list.

comment:17 Changed 12 years ago by David Kirkby

You beat me to it by 30 seconds. Here is what I had to say

The main buildbot page is here:

http://build.sagemath.org/sage/

The 'Waterfall display' seems the most interesting looking to me:

http://build.sagemath.org/sage/waterfall

  • fulvia is the Solaris x86 machine at Skynet
  • hawk (on far right) is my own personal OpenSolaris machine

I was not initially aware one could get the full log, but it is available. You have to click on the build stdio for the machine.

http://build.sagemath.org/sage/builders/fulvia%20full/builds/6/steps/shell_1/logs/stdio

The relevant bit is:

scipy_sandbox-20071020.p6/.hgignore
Finished extraction
****************************************************
Host system
uname -a:
SunOS fulvia 5.10 Generic_127128-11 i86pc i386 i86pc
****************************************************
****************************************************
CC Version
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.5.1/x86_64-SunOS-core2-sun-ld/libexec/gcc/i386-pc-solaris2.10/4.5.1/lto-wrapper
Target: i386-pc-solaris2.10
Configured with: /usr/local/gcc-4.5.1/src/gcc-4.5.1/configure --enable-languages=c,c++,fortran --with-gnu-as --with-as=/usr/local/binutils-2.20.1/x86_64-SunOS-core2-gcc-4.4.3/bin/as --with-ld=/usr/ccs/bin/ld --with-gmp=/usr/local/gmp-5.0.1/x86_64-SunOS-core2-gcc-4.5.0-abi32 --with-mpfr=/usr/local/mpfr-3.0.0/x86_64-SunOS-core2-gmp-5.0.1-gcc-4.5.0-abi32 --with-mpc=/usr/local/mpc-0.8.2/x86_64-SunOS-core2-mpfr-3.0.0-gmp-5.0.1-gcc-4.5.0-abi32 --prefix=/usr/local/gcc-4.5.1/x86_64-SunOS-core2-sun-ld
Thread model: posix
gcc version 4.5.1 (GCC) 
****************************************************
./spkg-install: FC=/home/buildbot/build/sage/fulvia-1/fulvia_full/build/sage-4.6.alpha3/local/bin/sage_fortran: is not an identifier

real    0m0.017s
user    0m0.001s
sys     0m0.005s
sage: An error occurred while installing scipy_sandbox-20071020.p6

I can now see what is wrong:

export FC="${SAGE_LOCAL}/bin/sage_fortran"
export F77="${SAGE_LOCAL}/bin/sage_fortran"
export F90="${SAGE_LOCAL}/bin/sage_fortran"
export F95="${SAGE_LOCAL}/bin/sage_fortran"

is a bashism - using export on the same line. But the spkg-install script starts with:

#!/bin/sh

The Solaris /bin/sh will not accept that syntax. (On OpenSolaris, a newer shell is used, which is why it worked on my machine).

I've opened #10106 to address this. One could get around it by changing the shell used in the spkg-install, but personally I prefer to write code in a more portable fashion, so I'll change that later today. I've very tired and must get some sleep, so it will have to wait for 8 hours or so, unless someone else wants to beat me to it.

Dave

comment:18 Changed 12 years ago by David Kirkby

I've updated #10106 to a blocker, but I have not slept yet and it is 5:25 am here!! I need some sleep.

Dave

comment:19 Changed 12 years ago by David Kirkby

I'll do this now, perhaps someone can review it in 15 minutes or so.

comment:20 Changed 12 years ago by David Kirkby

#10106 iss now ready for review - I have check it on fulvia to be sure it worked.

Dave

comment:21 Changed 12 years ago by Mitesh Patel

Merged in: sage-4.6.alpha3

It worked for me.

comment:22 Changed 12 years ago by Mitesh Patel

Milestone: sage-4.6.1sage-4.6
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