Archive forJune, 2011

Migrating SYBYL

SYBYL is a proprietary product from Tripos. It provides a whole bunch of intuitive molecular modeling for life scientists who are interested in drug and design. You need to buy a copy from them and get the license manager file made or get the license manager file from another user.

Requirements: Migrate an existing instance of SYBYL from one machine to another, using the same license file.

The initial installation of SYBYL was being carried out, by the vendor itself (since it was in support) on RHEL 4, wherein they have done all the installation including support, creating the license etc. But since the machine in which it was installed is no longer functional, we had to urgently shift it to a new machine.

The migration process is as stated below:

1. Got a new machine and installed CentOS 5.6.
2. Created a new user `tripos`, since SYBYL uses are normal user for the installation.
3. Copy the license manager file from the old machine to the new one.
4. Open the license file and check for the name of the machine as well as the mac address. The line would look like this,

SERVER sybyl.example.com 000f2c3de043

From the above line you can see figure out that the old sever name was `sybyl.example.com` and the mac address is `00:0f:2c:3d:e0:43`
5. Change the hostname of your new computer using the `hostname` command. You need to be root user while using this command,

hostname sybyl.example.com

6. Change the hardware Ethernet address of your new machine to that of your old one. You need to be the root user while using the following,

ifconfig eth0 hw ether 00:0f:2c:3d:e0:43 up

7. Copied all the 4 CD’s to the installation directory
8. Go inside CD1 and do the following,

sh install.sh

9. A GUI will pop up which will show your way to the next steps.
10. Path of the old license file.
11. In case you plan to have the other databases installed go on else click on exit after your basic installation.
12. Read the `ToDoList.txt` inside the `sybyl7.2` directory
13. Start the SYBYL license manager using the following commands,

cd trigo
- Enter: trigo -shell sybyl7.2
- Enter: su (enter root password when prompted)
cd $TA_LICENSE/bin/unix
cp ./triposlm.sh /etc/init.d/triposlm.sh
/etc/init.d/triposlm.sh -up
exit
exit

14. Once the license manager is started you can use the sybyl software. The binaries will be kept in sybyl7.2/bin/linux

Note: There might be errors, which might crop up while running sybyl. I have listed some of them,

Error 1: sybyl7.2/bin/linux/autoterm.exe: error while loading shared libraries: libXm.so.3: cannot open shared object file
Error 2: sybyl7.2/bin/linux/autoterm.exe: error while loading shared libraries: libGL.so.1: cannot open shared object file
Error 3: sybyl7.2/bin/linux/autoterm.exe: error while loading shared libraries: libGLU.so.1: cannot open shared object file
Error 4: sybyl7.2/bin/linux/autoterm.exe: error while loading shared libraries: libGLU.so.1: wrong ELF class: ELFCLASS64

As part of the solution 1,2 and 3 you need to install the following,

yum install openmotiff22 mesa-libGLU-6.5.1-7.8.el5.i386

Error 4 came up, since I was installing a 32 bit application on a 64 bit machine.

In case you have any more dependencies, you can use the following command,

yum whatprovides library-name

After all the installation is done, you are done good to run sybyl.

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Ride to Nrityagrama

Participants:

1. Shrikant Gaikwad
2. Srinivas R.
3. Wife (Chumki) and Myself

Date: 12th June, 2011

Mode of Transport: Bajaj Platina 125 cc, Unicorn

Nrityagram is a residential school for Indian classical dances and an intentional community in the form of a dance village, set up by Odissi danseuse Protima Gauri in 1990. It is situated near the Hesaraghatta Lake at a distance of about 35 kms from Bangalore.

The most noticeable thing that you would find is that of a students life style. They seem to follow the age old tradition of taking care of the Guru’s. As per this ancient method, students look after and care for their master by growing fruit and vegetables on the land, cooking, cleaning, and earning through dance recital.

Route Information:

The place is around around 35kms from the main Bangalore city located besides the Hasarghatta main road via Jalahalli. Drive down the road till you reach the horticulture research centre and take a left from there. Move down little and take the first right towards “My Native Village”. Drive down further more and you can see a board to take the right towards the Nrityagram place. It would be around 5 kms from this point (a lone stretch, but too good).

The way is to go via Jalahalli -> Doda Byalakere -> Hasaraghatta -> Take right -> My Native Village -> Nrityagrama. Road condition is good.

Nrityagram

Nrityagram Hut

Temple at Nrityagram

Reference:

http://en.wikipedia.org/wiki/Nrityagram
http://www.nrityagram.org/

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