polymake 3.2 visulization error

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beew
Posts: 25
Joined: 13 Aug 2015, 20:41

Re: polymake 3.2 visulization error

Postby beew » 19 Feb 2018, 04:21

Probably this is a consequence of your incomplete installation stopped because of lacking write permissions. First fix that, then start polymake --reconfigure (just once, not every time). The visualization with jreality should work then.
Running polymake --reconfigure does solve the problem but only one time. If I restart polymake again without --reconfigure then the same error appears. so I have to do --reconfigure each time when I start polymake.

I don't think it has anything to do with lack of permission, I did make a mistake one time but I have recompiled polymake-3.2 several times and each time with a clean slate and use sudo before install . I rebuilt and reinstalled polymake3.1 (after removing everything in 3.2) then it works without issue.

beew
Posts: 25
Joined: 13 Aug 2015, 20:41

Re: polymake 3.2 visulization error

Postby beew » 19 Feb 2018, 08:32

I solved the problem! It is a bit convoluted

When re-installing polymake-3.1 I encountered a strange error
dpkg: error processing archive /home/beew/Downloads/polymake-3.1/polymake_3.1-1_amd64.deb (--install):
trying to overwrite '/root/.oracle_jre_usage/9e360713136aba0a.timestamp', which is also in package rstudio 1.1.423-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
After removing restudio polymake-3.1 installed smoothly and jreality worked too. I then removed polymake 3.1 and reinstalled 3.2, after that jreality stopped working unless I started polymake-3.2 with the option --reconfigure each time (not once)

I then removed polymake-3.2 (at this point, no polymake in the system left) to reinstall rstudio. Next I reinstalled polymake-3.1 and saw the same "trying to overwrite oracle_jre_usage" error again, so I did

Code: Select all

sudo dpkg -i --force-overwrite polymake_3.1-1_amd64.deb

I then removed polymake-3.1 again and installed polymake-3.2. After starting polymake-3.2 with --reconfigure once jreality always works! (rstudio also works)

It seems that when installing rstuido from source with sudo java created a timestamp in .root and that was the source of the problem. I could not have noticed this from installing polymake-3.2 because the installation went through smoothly. This seems to be an oracle issue since I never had this problem with openjdk (but it is buggy in Ubuntu 16.04 for other reasons) "dpkg -i force overwrite" appeared to clean that up.

Thanks for the hint about the reconfigure option.

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gawrilow
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Posts: 349
Joined: 25 Dec 2010, 17:40

Re: polymake 3.2 visulization error

Postby gawrilow » 19 Feb 2018, 09:54

Two hints for the future:

1. When you are going to use two different polymake versions in parallel, create separate configuration directories for them, e.g.:
POLYMAKE_USER_DIR=~/.polymake-3.1 polymake-3.1/bin/polymake
There may be significant differences between the versions with regard to the structure of configuration items; when you run an older version it may corrupt the configuration created by the newer one. polymake issues a warning in this case but this can be easily overlooked.

2. If you don't like a software installation spreading itself over your computer's filesystem, you might find the docker image more suitable. It does not leave any traces apart from a copy of resources in your ~/.polymake folder, and even those are automatically removed when you choose the uninstall option.

beew
Posts: 25
Joined: 13 Aug 2015, 20:41

Re: polymake 3.2 visulization error

Postby beew » 19 Feb 2018, 12:04

Two hints for the future:

1. When you are going to use two different polymake versions in parallel, create separate configuration directories for them, e.g.:
POLYMAKE_USER_DIR=~/.polymake-3.1 polymake-3.1/bin/polymake
There may be significant differences between the versions with regard to the structure of configuration items; when you run an older version it may corrupt the configuration created by the newer one. polymake issues a warning in this case but this can be easily overlooked.
I am not using two different polymake. I was uninstalling one and installing the other alternately in order to find out why jreality wasn't working in 3.2. At any one time there is at most one polymake.
2. If you don't like a software installation spreading itself over your computer's filesystem, you might find the docker image more suitable. It does not leave any traces apart from a copy of resources in your ~/.polymake folder, and even those are automatically removed when you choose the uninstall option.
docker has other problems. It doesn't integrate well with the system. e.g if I use a program to compile another. checkinstall is optimal. anyhow, I am able to build with ninja and install with checkinstall so that is not a problem.

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gawrilow
Main Author
Posts: 349
Joined: 25 Dec 2010, 17:40

Re: polymake 3.2 visulization error

Postby gawrilow » 19 Feb 2018, 12:35

I am not using two different polymake. I was uninstalling one and installing the other alternately in order to find out why jreality wasn't working in 3.2. At any one time there is at most one polymake.
Well, it was not parallel in the strict sense, maybe I should have called this "alternating". At any rate, both versions were reading and rewriting the same configuration files. While it's tested and supposed to be painless in general to upgrade the configuration to a newer version, it's much more unsafe to downgrade it.


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