Ubuntu Installation :: Compiling Pymol 1.4.1 Fails In 11.04 Runs Perfectly In 10.10
May 12, 2011
I like to keep my pymol molecular viewer as recent as possible. With svn and compiling it used to be easy, up until ubuntu natty. Now I get the following error every time I try to compile:
layer1/Scene.c: In function SceneClick:
layer1/Scene.c:4557:11: internal compiler error: in set_jump_prob, at stmt.c:2319
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.5/README.Bugs> for instructions.
error: command 'gcc' failed with exit status 1
This is for EVERY version I have tried. I have even downloaded the source code you can find in the ubuntu repositories (current version for 64 bit is pymol 1.2r2) and tried to compile that one, just as prove of concept. I still get the same error. I think I might need something else beyond what I have already, because if the package maintainers could build the older version for natty, I should be too, with the proper packages, shouldn't I?
I have an Ubuntu server running Couch Potato, Sick Beard and Sabnzbdplus. Everything "works" pretty well in a sense that CP and SB push the NZB's to Sabnzbdplus, but Sab crashes regularly (haven't found the solution or the cause for this problem, so if you have some advice regarding that, it's welcome).To counter this problem (Sab crashing) I have a script written which checks if Sab is runnning and if it isn't start it:
I've ditched ubuntu for xubuntu 11.04. I love it. The marvellous grid based desktop...the beautiful theme...the ease of customisation...everything. I switched because I didn't like unity.However, I now have a problem. After installing the proprietary ati drivers for my raedon 5xxx card, compz still does not work at all. A lot of other people have been having problems with extreme lag when dragging windows (my unity-likeing school friend included). I don't have this problem because compiz won't work. The weird thing is that in any other 3d tasks the card performs better than on 10.10. For example I can now play oblivion without the characters lacking faces.
I have two hard disks, the one that I work with and another one for backups. The main HD had an OS (Ubuntu) partition, a partition for /home and a lot of free space.I installed latest Mandriva creating a new partition. Everything OK. But it overwrote GRUB and I couldn't boot into Ubuntu, so I reinstalled GRUB from the Ubuntu live CD. I got my Ubuntu back, but then it wouldn't boot into Mandriva. Well, I didn't care. But now the problem comes.
Right now, if I try to install Ubuntu from live CD, the installer won't see the partitions in my main drive. It sees the partitions in the backup drive, but the main drive appears as empty, no Ubuntu, no Mandriva, and no /home. Debian testing installer did just the same. Those partitions are there and I can boot into them and see them; it's only the installer that does not see them.
I tried to install ubuntu 10.04 to a 16 gig thumb drive and the installation went perfectly. However, when I removed the thumb drive and tried to boot the computer back into windows I saw that the installer had installed GRUB on to the hard drive of the computer. Windows runs fine, but it wont start with out the thumb drive that has the ubuntu install on it, this is very bad for me. Is there a way I can remove GRUB with out messing up windows on the computer? i dont have a windows 7 boot disk so this operation would need to be done either in windows (already booted) or ubuntu.
I'm running PyMOL version 1.2r2 on Fedora 12 with python2.6.
Only for a second or two will molecular models display correctly in the PyMOL viewer, and then the image becomes distorted. As I rotate the model, it displays correctly, but then almost immediately after I stop moving the model, it becomes distorted again.
The attached images show the display before and after the distortion.
This is some of the information that the PyMol program prints as it loads.
I am converting over to linux ubuntu 11.04, and I have used it for a week, love it. I installed an old 30gb HDD in order to install it ubuntu to try it out. Now I want to erase my primary windows XP drive and reformat to ext4, just like linux. Is there any prog or method that will make a perfect copy of what I have on my current drive ubuntu and put it on the newly formatted drive primary, so that it can boot ubuntu will all of the stuff I have on it right now?
I am trying to compile systemc. Configuration is done OK and Makefiles are created. As soon as the "make" command i issue, recursively reaches the "utils" directory, errors are produced -declaration and include errors.
The files referenced by the errors DO exist and i hava managed to give g++ "-I ${LD_INCLUDE_PATH}, ie the variable, where all header dirs are listed. Libraries and compilers for gcc3.3 and g++3.3, i believe, are installed OK. code...
I am trying to install form source (gnome-voice-control-0.4.tar) the voice recognition tool. ./configure seems to go fine, the Makefile has been made bur when I try to install by typing make some errors appear.
code:
Quote: [root@piotr gnome-voice-control-0.4]# ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes[code].....
I'm using Vector Linux for years without any issues, But I'm really paining with configure X for perfect performance for my newly bought(only 1 month old) PC (which has the intel 845G graphic chip)
I also tried compiling the official driver from the Intel site but the compilation fails.After that I used i810 driver in xorg.conf, Its not stable and not reliable. Finally(even now) I'm using vesa driver,Its stable but I cannot play videos.video grabs always.
I just installed Ubuntu on a laptop that is running windows 7. I accidentally tried installing a piece of software from the software centre before setting up my network. When I boot Ubuntu it now runs in low graphics mode only.
I tried installing Ubuntu 9.10 using both Ubuntu Desktop CD and the Netbook Remix on a EEEPC 1005HA with an external CD drive.
In both cases I don't get any graphical interface during the installation. The CD is apparently installing everything silently, without letting me change anything on the way, and then it gets stuck.
The only screen I get is the first one, with the options to "try Ubuntu" or "install Ubuntu".
Am running karmic on a P2-350 Mhz with 256 Mb RAM. Yes, I know this is an old computer, but it has been very good, performance wise, since versions earlier than 8.x I think.
But now, after a fresh install of karmic, it is very slow at everything. Checked system monitor and CPU is constantly running at between 95% and 100%
It is a sad day indeed, but I need to run a developer's tool that only runs on Windows, and it interfaces with a USB device that doesn't do well through any VMs I've tried. I've resorted to installing XP.
Now, I'm wondering if there will be any problems I'll face installing XP after Ubuntu 10.04 has already been installed? I suspect so, but it's been a while since I dual booted, and I've never worked with Grub2,
so, I was just upgrading to the new release of Ubuntu and didn`t notice that laptop was running on battery, then it was switched off.Now I can open Ubuntu system, can`t reach to login page.the other two systems are ok, XP and Pardus.how do you think I can recover ubuntu?
Since support for 8.04 LTS will be ending soon, I decided to move up to 10.04 LTS. On my old Thinkpad A20m laptop, the install went well, and everything seemed to work except the middle trackpoint button. Fixed that easily by editing a conf file. Then I began to notice some problems; all power management options (suspend, idle timers, etc) have no effect. I checked the startup logs and it seems that ACPI was not loading due to my aged bios (yes it's the newest version available). I tried using acpi=force in the boot options, and viola: power management is working. But that made two other problems crop up.
Problem 2: Since using acpi=force, the laptop runs so hot it sometimes gets sluggish and locks up. I tried installing "thinkfan" from the ubuntu repositories to have some way of easily changing the fan behavior(which I believe relies on ACPI in some fashion). No luck there. ACPI seems to not see my fan at all, and it only kicks on when the bios high temp failsafe is tripped. I should also mention I am using Xubuntu (for the lighter desktop). I'm still kind of an Ubuntu-noob, so I wasn't sure what other info to post.
I had F11 i586 installed on my X86_64 machine. I used preupgrade to move up to F12. (I had the space problems noted elsewhere, but eventually got all of the F12 packages installed.) Grub now has the following titles:
Fedora (2.6.31.5-127.fc12.i686) Upgrade to Fedora 12 (Constantine) Fedora (2.6.30.9-96.fc11.i586)
If I boot to F12, it boots up to a point where I get garbage graphics and the system freezes. If I boot to F11, SELinux relabels and the system then boots normally. I'd like to boot normally into F12.
Yesterday I downloaded 10.10 desktop version and burned an image to a CD. After installed to a Dell Dimension E510 machine successfully (I wiped out windows completely), the first update found 315 items to update. After downloaded, ubuntu asked to reboot the machine. Since then, the machine is stucking on the ubuntu startup screen. I suppose it is applying the updates; however, it has been over 12 hours. Is it normal to take that long?
It seems I had no say in the matter. The installer automatically did text mode and it starts up in text mode now. I'm very new to Fedora, though I had Ubuntu installed recently but removed it because Fedora seemed a little more interesting to me. I'm on an HP Pavilion dv2807nr laptop if that helps.
I've just upgraded my from F11 to F12 via software update and found F12 extremely slow to the extent that only the mosue cursor moves, the rest does not - not even opening folders or starting application.
My specs: Core2Duo 1GB RAM 160GB HDD
It seems that
npviewer.bin is taking up up to 50% of CPU. Xorg takes 20%..
I am trying to install FC 10 from a DVD. It gets to part where it says "Running Anaconda" and the monitor goes "no signal". I am assuming that the video drivers are incorrect. What can I do to change the drivers before anaconda runs?
Can any one tell me how to configure Tomcat ldap URL authentication perfectly? I've tomcat installed with port forwarding to http(80). I could able to confiure apache ldap authentication. For this i modified the file '/etc/apache2/sites-enabled/000-defaults' with the DocumentRoot /var/www.
But for tomcat '/usr/share/tomcat/webapps' I could not able to configure 'server.xml' file perfectly.
I recently installed Ubuntu 10.10 on my Sony Vaio VPCEE2E1E. I've been able to avoid any major problems, however, my onboard sound doesn't work. I've tried plugging speakers into the laptop and this works perfectly. I'm rather confused as to why the onboard sound isn't working though.
Here's the output for lspci on my machine:
Code: **** List of PLAYBACK Hardware Devices **** card 0: SB [HDA ATI SB], device 0: ALC259 Analog [ALC259 Analog] Subdevices: 1/1 Subdevice #0: subdevice #0 card 1: HDMI [HDA ATI HDMI], device 3: ATI HDMI [ATI HDMI]
If I click the network indicator and select Connection Information, I get a dialog that says "Error displaying connection information: No valid active connections found." If I click Edit Connections, it shows Auto eth0 as "Never used". Yet I am using my network connection right now. If I download something, I am getting full performance. I am surfing the net and posting this, now.What has happened to my connection info and how can I fix it?
My computer runs Karmic and has quit booting when it is plugged in. I was told it was the AMP needing updated. How do I do that? I do the updates from the update manager, does this mean I missed the AMP update or is it done differently than through the update manager.
I need help creating a barebones version of linux that has just python & QT on a frame buffer, which only runs on 16mb of ram & can be loaded on a 32mb flash drive.
I can browse smoothly without any speed problems at all but all update stuff like apt-get , software centre etc get stuck. As in they get 0kbps fr lk a long time n then move on n then agn 0kbps. Until the downlaod is done!
practically out of the box in U10.10, well modulo a little tweak to force /dev/video0 as the default webcam... (as I have a PCI capture card)...Both upgrade from 10.10 or fresh install of 11.04, in 11.04 sn9c202 fails to work on most webcam apps, apart from xawtv...
