How do I use the PVM command line console?
Once you have set the environment variable
$PVM_ROOT
you can start the PVM console using the following command:
$PVM_ROOT/lib/pvm
The 'setenv' command in the console will generate a listing of the local environment set in PVM.
The 'conf' command will tell you which hosts are currently present within your virtual machine.
If there are problems with a specific node, try the command
add <node-name>
and see if it generates an error.
What do I need to do in order to use parallel GOLD with my own in-house installation of PVM?
In some circumstances, users may prefer to run parallel GOLD using a pre-existing installation of PVM rather than the version
packaged within the UNIX GOLD installer. However, this can cause difficulties since the parallel components of GOLD are compiled
against the version of PVM packaged with GOLD using specific compiler flags.
If the user's version of PVM is significantly different, parallel GOLD may not function correctly in its default configuration.
The solution is for the user to re-compile the PVM parts of GOLD on their system. For this reason, the UNIX GOLD distribution is packaged
with a tar-gzip patch file for the parallel version that allows parallel GOLD users to recompile the PVM part of GOLD on their system.
It also recompiles the front end and the pvm shared object used in the main gold process.
If you would like try recompiling the parallel components of GOLD on your own system, you will find the required patch file here:
$GOLD_DIR/gold_pvm_patch.tar.gz
Please unpack this file and consult the ReadMe file for further details.
How do I set up passwordless SSH access between the nodes in my PVM cluster?
To run parallel GOLD using PVM, passwordless shell access (either RSH or SSH) must be set up between all of the machines that you wish to use in your PVM
cluster.
RSH is far easier to configure for use with PVM, since it can operate without special configuration on each host that you wish to access.
However, some users have difficulty configuring RSH access on their systems. RSH access usually fails because the RSH option has been disabled on
your system. This is usually done by the systems administrator because RSH works without any host-to-host authentication and is therefore not very secure.
SSH is more secure since it uses host-to-host authentication, but it means that you have to configure your system for your user account(s)
to use this secure protocol. Here is a set of instructions for setting up passwordless SSH access between two machines. We will call the machine
you are using to set up and run the GOLD jobs the "master", and the machine you wish to access using SSH the "slave".
Firstly, log on to the master, change to your home directory and generate a key pair by typing
ssh-keygen
When it asks you for a pass-phrase leave it blank. This will create you a pair of files, one called "identity.pub" by default,
in the directory ".ssh".
Copy your "public key" (e.g. identity.pub) onto the slave machine. You can do this with the following command:
scp ~/ssh/identity.pub <username>@<slave machine>:~/identity.master
For example:
scp ~/ssh/identity.pub joe@joes-machine.ournet.dom.country:~/identity.master
Log into the slave machine using this command:
ssh -l <username> <slave machine>
For example:
ssh -l joe joes-machine.ournet.dom.country
You will be asked for your password on the slave machine. Copy the master key (i.e. in the file identity.master in your home directory)
into the slave's authorized keys file using the following command:
cat ~/identity.master >> ~/.ssh/authorized_keys
You may need to create the ~/.ssh/authorized_keys file first. Then log out, back to the master machine.
Check you can log into the slave without a password:
ssh -l <username> <slave machine>
For example:
ssh -l joe joes-machine.ournet.dom.country
You should now be able to access the slave without a password. To set up passwordless access to the master from the slave,
you need to repeat the above procedure but treating the master as the slave and vice versa.
To get PVM to work with SSH you need to set a global environment variable $PVM_RSH to ssh on all systems that you intend
to use in the PVM cluster.
For example, if you use the C-shell (csh) as your default shell, in your ".cshrc" file you need to add the following line:
setenv PVM_RSH ssh
Why is there a discrepancy between the final fitness score and the calculated fitness score (from individual terms) of a docking performed using the GOLD API?
Under some circumstances when using the GOLD API there may be a discrepancy between the calculated fitness score and the final fitness score displayed in the ligand log file. For example, the ligand log file may contain something like this:
GOLD fitness breakdown of terms:
Fitness = S(hb_ext) + 1.3750*S(vdw_ext) + S(hb_int) + 1.0000*S(vdw_int) + S(cust)
Fitness S(hb_ext) S(vdw_ext) S(hb_int) S(vdw_int) S(cust)
73.02 17.94 28.28 0.00 -3.73 3.32
The S(cust) term may have been incorrectly included in the
final fitness score more than once. Such a discrepancy could be due to a known
issue with the GOLD API. For reasons of efficiency, the fitness is not always recalculated,
but sometimes simply copied if no changes have been made to an individual
during a previous iteration of the GA. To resolve this issue, GOLD must be prevented from re-adding the custom_score term.
For further advice and assistance, please contact User Support.
Why does GOLD 4.1
take many minutes to start?
This issue can occur if Hermes cannot contact the default CCDC
IsoStar server and has to go through a proxy server to do so.
This bug is fixed in GOLD
Suite
1.3.1 - GOLD will now check for the
environment variables HTTP_PROXY and HTTP_PROXY_AUTH. The syntax
expected for these environment variables is:
HTTP_PROXY=http://‹host›:‹port›
or
HTTP_PROXY=http://‹user›:‹password›@‹host&rsa$
HTTP_PROXY_AUTH=basic:*:‹user›:‹password›
Note that the basic:* component of HTTP_PROXY_AUTH is ignored, only
the ‹user›:‹password› component is used.
