Sage Crash Report

[Kashif Bari]

I am trying to install Sage version 8.9 on the High performance cluster at my university, which runs Linux (CentOS 7). I am installing to my local "scratch" folder since I do not have administrative permissions. I am trying to install from source code as the pre-built binaries are for Ubuntu and Debian and did not work for me and I was unsure if they would work on CentOS 7. I was able to run ./configure without any issues and then when i did make, I received the following log file (attached) and error: 

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package: mpfr-4.0.1.p0
  log file: /scratch/user/kbari/sage-8.9/logs/pkgs/mpfr-4.0.1.p0.log
  build directory: /scratch/user/kbari/sage-8.9/local/var/tmp/sage/build/mpfr-4.0.1.p0

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make[1]: *** [all-start] Error 1
make[1]: Leaving directory `/scratch/user/kbari/sage-8.9'
make: *** [all] Error 2

 I have tried to contact the help and support for the cluster, but they do not know much about Sage. Any help would be greatly appreciated! Thank you for your time!

[Isuru Fernando]

One alternative to installing sage is by using the conda package manager. https://github.com/conda-forge/miniforge#download

It's know to work on CentOS 6 and above.

See https://github.com/conda-forge/sage-feedstock#installing-sage

Isuru

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[kash...@gmail.com]

Hi!

 Thanks for responding! Will this require any administrative permissions? I do not have any sudo privileges. 

On Mar 18, 2020, at 6:48 PM, Isuru Fernando <isu...@gmail.com> wrote:



To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CA%2B01voPejK9ynCNn_JFUGWcA%3DP4X4wM2bjdpCF8fk%2Bw1Ft-KPw%40mail.gmail.com.

[Isuru Fernando]

No, it doesn't require sudo privileges. It can be installed in your home directory.

Isuru

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/5F5071CF-92DB-426A-A758-858CDA89EA00%40gmail.com.

[kash...@gmail.com]

Thank you!

Best,

Kash

On Mar 18, 2020, at 6:48 PM, Isuru Fernando <isu...@gmail.com> wrote:



To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CA%2B01voPejK9ynCNn_JFUGWcA%3DP4X4wM2bjdpCF8fk%2Bw1Ft-KPw%40mail.gmail.com.

[Dima Pasechnik]

mpfr needs makeinfo program to be installed. This is a pretty standard thing,
which on Centos is in texinfo package
https://centos.pkgs.org/7/centos-x86_64/texinfo-5.1-5.el7.x86_64.rpm.html


By the way, why are you building Sage 8.9, and not 9.0?

[Kashif Bari]

Thank you, Dima, I was able to load the texinfo package before I did make and I believe this resolved my issue with mpfr. However, I ran into the same issue with mpc-1.1.0 now instead of mpfr.

I currently have sage 8.9 installed on my personal laptop, so I figured I would stick with the same version that I know my code runs on.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq0p1Z5t8KZmWvPqdqstOS77eaLveTs5w8qsOXp6EwK67w%40mail.gmail.com.

[Dima Pasechnik]

On Thu, Mar 19, 2020 at 12:25 PM Kashif Bari <kash...@gmail.com> wrote:
>
> Thank you, Dima, I was able to load the texinfo package before I did make and I believe this resolved my issue with mpfr. However, I ran into the same issue with mpc-1.1.0 now instead of mpfr.

hmm, the same? If you have now makeinfo installed, it should be a
different issue.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAJoD6MJFKbvovOSj_zLpBohUPtaPFYP%3Dpx8XKza5Lhb%2ByAiqFA%40mail.gmail.com.

[Kashif Bari]

I believe I was able to resolve the issue with mpc-1.1.0 by loading a more recent version of the texinfo package! Hopefully others who have this issue will be able to resolve it similarly.

However, I ended up running into this issue when running make again:

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package: sqlite-3270100
  log file: /scratch/user/kbari/sage-8.9/logs/pkgs/sqlite-3270100.log
  build directory: /scratch/user/kbari/sage-8.9/local/var/tmp/sage/build/sqlite-3270100

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [all-start] Error 1

It seems CentOS doesn't like when I install Sage! Thank you all once again for all your helpful comments!

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq1iCUYRzukvrD95DKgg%3DtJhLoDHcDEmZiddwG%2BGADCDgg%40mail.gmail.com.

[Dima Pasechnik]

On Tue, Mar 24, 2020 at 4:51 PM Kashif Bari <kash...@gmail.com> wrote:
>
> I believe I was able to resolve the issue with mpc-1.1.0 by loading a more recent version of the texinfo package! Hopefully others who have this issue will be able to resolve it similarly.
>
> However, I ended up running into this issue when running make again:
>
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: sqlite-3270100
> log file: /scratch/user/kbari/sage-8.9/logs/pkgs/sqlite-3270100.log
> build directory: /scratch/user/kbari/sage-8.9/local/var/tmp/sage/build/sqlite-3270100
>
> The build directory may contain configuration files and other potentially
> helpful information. WARNING: if you now run 'make' again, the build
> directory will, by default, be deleted. Set the environment variable
> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
>
> make: *** [all-start] Error 1
>

this is a familiar problem, due to skew clocks on your system, I suppose.
Is /scratch/ a local filesystem? If not, you'd better try building on
a local filesystem.
(the problem is that sq
In the upcoming release one should be able to use sqlite from the system,
thanks to https://trac.sagemath.org/ticket/29002

One way around this should be to change the line

sdh_configure

near the bottom of build/pkgs/sqlite/spkg-install

to be

sdh_configure --disable-maintainer-mode

and try again running make again.

(This change should make sqlite's ./configure less sensitive to skew clock)

HTH,
Dima

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAJoD6M%2BXkyeCsj9wpgCfVXU52YMoOrLUMZ1Je4F7in4orW1iqw%40mail.gmail.com.

[Kashif Bari]

Hi Dima,

I am building locally, as this is a university cluster and I only have access to my local directories.

Unfortunately, this did not resolve the issue and this line was added to my output:

[sqlite-3270100] configure: WARNING: unrecognized options: --disable-maintainer-mode

In the log file, it still has this as the last error: 

configure: error: in `/scratch/user/kbari/sage-8.9/local/var/tmp/sage/build/sqlite-3270100/src':

configure: error: C compiler cannot create executables

Best,

Kash

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq31HJwhzkzSwAVzG32d_ahfPARm%3DHja41ze%3D3yxC5F10w%40mail.gmail.com.

[Dima Pasechnik]

On Wed, 25 Mar 2020, 02:21 Kashif Bari, <kash...@gmail.com> wrote:

Hi Dima,

I am building locally, as this is a university cluster and I only have access to my local directories.

by "local" I mean the filesystem on a disk physically in the machine you are using,

as opposed to a networked file system, often used on HPC clusters.

HPC clusters usually give users space for their home directories on networked file systems, and for "scratch" partitions too.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAJoD6MLgEfp_0WHwA2GpQykbMoij5UUi-nyeYvDwmbTfe6CJZg%40mail.gmail.com.

[Kashif Bari]

I do not believe I I have permissions to build on a disk physically in the machine being used. The scratch folder is where I was told to install any software that I wish to use. The home directory that I have is not large enough to install anything.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq2svfW3SQDi%2BOUW%3DGF4eMjvQvOG5HU0fBb7Jh-5siGBgQ%40mail.gmail.com.

[Dima Pasechnik]

On Wed, 25 Mar 2020, 14:19 Kashif Bari, <kash...@gmail.com> wrote:

I do not believe I I have permissions to build on a disk physically in the machine being used.

you may ask for, at least, explaining that you have a problem with skew timestamps.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAJoD6MKLZtAd1bkA0qLKzcuLt5gQ11%3D7FYkUaUzB-JRGLMEZ6A%40mail.gmail.com.

[Dima Pasechnik]

Also, sqlite has been updated in sagemath 9.0, as well as we have there

https://trac.sagemath.org/ticket/28511

which is meant to help with skew clock issues.