Author Topic: Ubuntu + PixinSight  (Read 6957 times)

Offline Eli

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Ubuntu + PixinSight
« on: 2008 July 28 07:38:08 »
Hi,

I have been using PixInsight for about 6 months and have recently upgraded to Ubuntu Hardy Heron. Unfortunately, PixInsight crashes every time I use it now. Is this is a known issue?

Thanks,

Eli

Offline Juan Conejero

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Ubuntu + PixinSight
« Reply #1 on: 2008 July 29 00:14:47 »
Hi Eli,

Are you using the new version 1.2 of PixInsight? If not, it's important that you download and install it.

If you are using an older version (< 1.2) and a 64-bit operating system, the PixInsight Core application crashes due to an issue with DEP (Data Execution Prevention). In this case the only solution is disabling DEP temporarily during application startup. Of course, the new 1.2 doesn't have this problem, and also introduces 64-bit versions that can be used on 64-bit systems.

Finally, chances are that the new Ubuntu lacks some symbolic links that are necessary to load required system libraries. Other users have had the same problem, and we have fixed them easily by creating the lacking links manually. To know if this is your case, please execute the following commands from a terminal console:

Code: [Select]
cd /<directory_where_pi_is_installed>/bin
export LD_LIBRARY_PATH=.; ldd PixInsight-core


This will show you all the required libraries and their default locations. For example, this is the output on my Fedora 8 x86_64 machine:

Code: [Select]
[juan@cygnus bin]$ export LD_LIBRARY_PATH=.; ldd PixInsight-core
        linux-vdso.so.1 =>  (0x00007fff4affd000)
        liblcms.so => ./liblcms.so (0x00002aaaaaaad000)
        libjs.so => ./libjs.so (0x00002aaaaacea000)
        libzlib.so => ./libzlib.so (0x00002aaaaafcc000)
        libcfitsio.so => ./libcfitsio.so (0x00002aaaab1e3000)
        liblibtiff.so => ./liblibtiff.so (0x00002aaaab5a6000)
        libjpeg.so => ./libjpeg.so (0x00002aaaab806000)
        libSM.so.6 => /usr/lib64/libSM.so.6 (0x00000030b3000000)
        libICE.so.6 => /usr/lib64/libICE.so.6 (0x00000030b3400000)
        libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000030b1c00000)
        libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00000030b1400000)
        libXrandr.so.2 => /usr/lib64/libXrandr.so.2 (0x00000030b1800000)
        libXfixes.so.3 => /usr/lib64/libXfixes.so.3 (0x00000030b4800000)
        libXcursor.so.1 => /usr/lib64/libXcursor.so.1 (0x00000030b4400000)
        libXinerama.so.1 => /usr/lib64/libXinerama.so.1 (0x00000030b3c00000)
        libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00000030b0800000)
        libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00000030b1000000)
        libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000030b0400000)
        libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000030afc00000)
        libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00000030b4000000)
        librt.so.1 => /lib64/librt.so.1 (0x00000030b2400000)
        libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00000030b2800000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00000030ae800000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00000030ae400000)
        libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00000030b9800000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00000030b5000000)
        libidn.so.11 => /usr/lib64/libidn.so.11 (0x00000030bc000000)
        libssl.so.6 => /lib64/libssl.so.6 (0x00000030bc800000)
        libcrypto.so.6 => /lib64/libcrypto.so.6 (0x00000030bbc00000)
        libldap-2.3.so.0 => /usr/lib64/libldap-2.3.so.0 (0x00000030bd000000)
        libz.so.1 => /lib64/libz.so.1 (0x00000030b2000000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000030b3800000)
        libm.so.6 => /lib64/libm.so.6 (0x00000030ae000000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000030b2c00000)
        libc.so.6 => /lib64/libc.so.6 (0x00000030adc00000)
        liblber-2.3.so.0 => /usr/lib64/liblber-2.3.so.0 (0x00000030b9c00000)
        libexpat.so.1 => /lib64/libexpat.so.1 (0x00000030b0c00000)
        libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000030af000000)
        libxcb-xlib.so.0 => /usr/lib64/libxcb-xlib.so.0 (0x00000030af400000)
        libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000030af800000)
        libselinux.so.1 => /lib64/libselinux.so.1 (0x00000030b0000000)
        /lib64/ld-linux-x86-64.so.2 (0x00000030ad800000)
        libgssapi_krb5.so.2 => /usr/lib64/libgssapi_krb5.so.2 (0x00000030bb400000)
        libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x00000030bb000000)
        libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x00000030ba000000)
        libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000030c3600000)
        libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000030aec00000)
        libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x00000030ba400000)
        libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000030bb800000)
        libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000030bd400000)


You should see no libraries with the following indication:

Code: [Select]
=> not found

If you see some of these, then here's the problem and we'll work to solve it.

Thank you for your patience. Unfortunately, Linux has these idiosyncrasies, but its performance and freedom always pay off.
Juan Conejero
PixInsight Development Team
http://pixinsight.com/

Offline Eli

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update
« Reply #2 on: 2008 July 30 11:22:49 »
Hi,

Thanks for the help. I'm currently using the 1.2 version of PixInsight with Ubuntu Dapper. I tried out the export command in the ./bin folder and got the following:

Code: [Select]

linux-gate.so.1 =>  (0xb7f44000)                                        
        liblcms.so => ./liblcms.so (0xb7efe000)                                
        libjs.so => ./libjs.so (0xb7e13000)                                    
        libzlib.so => ./libzlib.so (0xb7dfc000)                                
        libcfitsio.so => ./libcfitsio.so (0xb7c41000)                          
        liblibtiff.so => ./liblibtiff.so (0xb7be0000)                          
        libjpeg.so => ./libjpeg.so (0xb7bb4000)                                
        libSM.so.6 => /usr/lib/libSM.so.6 (0xb7b94000)                          
        libICE.so.6 => /usr/lib/libICE.so.6 (0xb7b7b000)                        
        libXrender.so.1 => /usr/lib/libXrender.so.1 (0xb7b73000)                
        libXrandr.so.2 => /usr/lib/libXrandr.so.2 (0xb7b6d000)                  
        libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0xb7b68000)                  
        libXcursor.so.1 => /usr/lib/libXcursor.so.1 (0xb7b5f000)                
        libXinerama.so.1 => /usr/lib/libXinerama.so.1 (0xb7b5c000)
        libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7aeb000)
        libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb7ac1000)
        libXext.so.6 => /usr/lib/libXext.so.6 (0xb7ab3000)
        libX11.so.6 => /usr/lib/libX11.so.6 (0xb79cc000)
        libgthread-2.0.so.0 => /usr/lib/libgthread-2.0.so.0 (0xb79c7000)
        librt.so.1 => /lib/tls/i686/cmov/librt.so.1 (0xb79be000)
        libglib-2.0.so.0 => /usr/lib/libglib-2.0.so.0 (0xb790c000)
        libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0xb78f4000)
        libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb78f0000)
        libcom_err.so.2 => /lib/libcom_err.so.2 (0xb78ed000)
        libresolv.so.2 => /lib/tls/i686/cmov/libresolv.so.2 (0xb78da000)
        libidn.so.11 => /usr/lib/libidn.so.11 (0xb78a9000)
        libssl.so.6 => /usr/lib/libssl.so.6 (0xb7866000)
        libcrypto.so.6 => /usr/lib/libcrypto.so.6 (0xb771a000)
        libldap-2.3.so.0 => /usr/lib/libldap-2.3.so.0 (0xb76da000)
        libz.so.1 => /usr/lib/libz.so.1 (0xb76c5000)
        libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb75d2000)
        libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb75ad000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb75a1000)
        libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7452000)
        liblber-2.3.so.0 => /usr/lib/liblber-2.3.so.0 (0xb7445000)
        libexpat.so.1 => /usr/lib/libexpat.so.1 (0xb7424000)
        libXau.so.6 => /usr/lib/libXau.so.6 (0xb7421000)
        libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb741e000)
        libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7406000)
        libselinux.so.1 => /lib/libselinux.so.1 (0xb73ed000)
        /lib/ld-linux.so.2 (0xb7f45000)
        libpcre.so.3 => /usr/lib/libpcre.so.3 (0xb73c6000)
        libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0xb73af000)
        libgnutls.so.13 => /usr/lib/libgnutls.so.13 (0xb7338000)
        libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7333000)
        libtasn1.so.3 => /usr/lib/libtasn1.so.3 (0xb7323000)
        libgcrypt.so.11 => /lib/libgcrypt.so.11 (0xb72d6000)
        libgpg-error.so.0 => /lib/libgpg-error.so.0 (0xb72d2000)


Looks good to me. except for the 8th from the bottom line. Suggestions?

Thanks,

Eli

Offline Juan Conejero

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Ubuntu + PixinSight
« Reply #3 on: 2008 July 30 11:34:20 »
Hi Eli,

Your ldd output shows no problem at all.

You are running a 32-bit (x86) operating system. Are you trying to run a 64-bit version of PixInsight?

You must download and install the following archive:

PI-x11-x86-01.02.00.405-20080716-c.tar.gz

*not* this one:

PI-x11-x86_64-01.02.00.405-20080716-c.tar.gz

which is for x86_64 systems.

Does this make any sense?
Juan Conejero
PixInsight Development Team
http://pixinsight.com/

Offline Eli

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no 64 system
« Reply #4 on: 2008 July 31 07:46:43 »
Hi,

I have a 32 bit system and I was running a 32 bit version of PixInsight. To be sure, I downloaded the program again and the same problem arises. When I was stretching a FITS file it crashed. This is generally where it keeps crashing as it is my first step to work on images. I'm quite perplexed about the problem. I have been using Linux distros for years and never had so many problems with a program. I may end up backing up my data and do a fresh installation.

Cheers,

Eli

Offline twade

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Ubuntu + PixinSight
« Reply #5 on: 2008 July 31 10:03:52 »
Eli,

Quote
When I was stretching a FITS file it crashed.


Although, I'm not running any Linux versions, it seems like PixInsight is having difficulty creating the "scratch" files.  What directory are the temporary or scratch files being saved to?  You can find this information in the Preferences dialog.  Does the directory exist?  Do you have permission to write to the directory?  I have found most problems with Linux are permission oriented.  How did you install the program (e.g. as root or local user)?  I would also check the permissions on the library files.

Wade

Offline Juan Conejero

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« Reply #6 on: 2008 July 31 11:08:12 »
Hi Eli and Wade

This is a very strange problem that I haven't seen before. It's true that such behavior might be related to insufficient permissions. However the core application should show error messages in this case, which I assume are not shown.

By default PixInsight writes all temporary files (swap files and autosaved psm files) to the /tmp directory. This is a standard directory that should be present in every Linux/UNIX system, and all users are supposed to have full read/write rights on it.

In the event that /tmp isn't available, PixInsight will use the ~/tmp directory (a tmp directory under the user's personal directory) if it exists, and as a last resort, it would use its own installation directory (which obviously exists). A real-world scenario where PixInsight is unable to write temporary files is very unlikely.

I suspect that this problem might be related to some system library that is incompatible (or causes problems) with other libraries upon which it depends. This is not too unlikely to happen on Linux. A frequent reason is updating the system too often (e.g., automatic updates enabled).

I have several questions to help locating the cause of this problem:

1. Describe your hardware. I am interested in knowing your processor model and number of processors, your motherboard brand/model if possible, your video card brand/model, and the amount of RAM you have installed. Of secondary interest is the size of your hard disk and the free space available on your local filesystem; I assume you have enough space.

2. Try to find a correlation between your upgrade to Ubuntu Dapper and the problems with PixInsight. Three related sub-questions:

2.1 Did you made a fresh installation from scratch, or did you upgrade a working system?. The latter is a *very bad idea*. A fresh installation is actually mandatory, especially with new Linux distributions.

2.2 If you install an old version 1.1.x that was working on your old Linux distro, does it cause problems also with your new Ubuntu Dapper?

2.3 Did you install PixInsight 1.2 on your old distribution? If yes, did it work well?

3. Run PixInsight from a terminal console. In this way we can see any warning messages printed on stdout if they occur, which might be of great help.

4. If you have another Linux box at hand, install and run PixInsight on it to see what happens. It would be great if you could try it on another Ubuntu Dapper installation, preferably a fresh one.

5. Try running PixInsight on the same machine but as a different user, if possible.

6. The idea of making a fresh installation isn't bad, either :)

We'll find and fix this problem. PixInsight is running on a variety of Linux distributions without flaws, so there's no reason why it shouldn't run on your Ubuntu.

Right now I am too busy with the new PixInsight 1.2.1 release, which is extremely important because it fixes some critical bugs. When I get more time, I'll try to install Ubuntu Dapper on a virtual machine and will explore it.
Juan Conejero
PixInsight Development Team
http://pixinsight.com/

Offline Eli

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directory
« Reply #7 on: 2008 July 31 11:09:51 »
Hi Wade,

The permissions are ok, since it's in a folder in the home directory. I installed the program as a local user and the directory and files are parametrized for local permissions. Thanks for the idea though. I will keep that in mind for the future.

Cheers,

Eli

p.s. I double checked the permissions just in case, it's all set for local user.

Offline Eli

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Ubuntu + PixinSight
« Reply #8 on: 2008 August 01 08:43:54 »
Here's are some answers to the series of the questions.

1. Specifications: Dual 2.4-GHz Xeon, 2GB RDRAM, 500 GB hard drive, nVidia Quadro4 64MB AGP  video card. I don't know what the motherboard brand is. It came with the system, a Dell Precision 530.

2. Upgraded the Ubuntu system. Version 1.1 worked on the old and new Ubuntu distro. Then after installing 1.2, it did not work anymore.  

3. The terminal output when it crashes
Code: [Select]
terminate called after throwing an instance of 'pcl::EUnixSegmentationViolation'

I don't have another distro nearby to test this, so I will be re-installing the OS sometime today or tomorrow. I will post an update on what happens afterward.

Thanks,

Eli

Offline David Serrano

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« Reply #9 on: 2008 August 28 05:15:15 »
Juan,

Quote from: "Eli"
3. The terminal output when it crashes
Code: [Select]
terminate called after throwing an instance of 'pcl::EUnixSegmentationViolation'


Some sort of stack trace would be totally useless to us mere mortals, but invaluable for you to further pinpoint the exact location of obscure bugs like this.

Just a quick suggestion off the top of my head :P.
--
 David Serrano