31 May 2011

4. Getting mouse and keyboard to work on Lenovo Thinkpad SL410 under Debian Testing/Wheezy

For the past few months (it seems) Debian Testing will install just fine on system. On the first boot, however, neither (internal or external) mouse nor keyboard will be responsive and to a casual observer it will appear that the system has hanged. This is fairly well documented and the solution is simple if you have an EXTERNAL keyboard and mouse available (but I'll show it here anyway):
1. Disconnect and reconnect your mouse and keyboard, or, on a laptop, connect a usb keyboard, so that you can log in.
2. Open the terminal  or a console (e.g. ctrl+alt+f1) and proceed to rename /run e.g. sudo mv /run /xrun

You could also delete the folder instead of renaming it. At this point you simply have to reboot and everything should be working without any reconnecting.

NOTE that everything will be responsive during the inital part of the boot - the mouse and keyboard do not stop working until startx/gdm3 starts.

If you do not have an external keyboard you would be advised to install openssh-server during the installation of Debian. This way you should be able to ssh to your laptop from another computer and fix it remotely.

I've set up four systems - three desktops and one laptop - using this approach, and all has been well. The past week a laptop that was set up this way suddenly booted into gdm3 with an unresponsive mouse and keyboard. Plugging in an external keyboard (which I do anyway to slow down the onset of carpal tunnel from using a keyboard at weird angles - I'm not much of a fan of touchpads either) made my laptop usable, but the problem has been annoying - a system which you use for work should be in, well, working order.

At any rate, the /run folder was back. I tried just removing /run/udev, and it didn't help. I couldn't easily remove /run, since it was locked, but by attaching the hdd to another system I could remove it. On boot I got a number of error messages saying that various folders under /var/run/ could not be accessed, and I never made it to either gdm3 or a console. Booting by selecting the 'rescue/recover' option in grub dropped me into a terminal, but I could little beyond creating a /run folder (sudo mkdir /run).

ls /var/run -lah showed that /var/run was linked to /run. /var/lock had also shown up in various error messages. I renamed the /var/run and the /var/lock files (xrun and xlock), made sure that there was no /run folder, and rebooted. Still not happy and no console - complains about various things missing. Booting using the recover option (or is it rescue? Whatever, you'll know when you see it) created the necessary files, but did not create a /run folder. Rebooting and selecting the normal startup option in grub now went off without a hitch, with gdm3 behaving and the touchpad working. It took a few nervous seconds after the start of gdm before the mouse became responsive, but work it did.

So, if you're having the same problem, and you haven't had much luck deleting /run, have a look at /var and see if there are any links.

Now, the big question is: why was /run recreated in the first place?
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28 January 2011

3. Compiling nwchem on Ubuntu 10.10 64 bit

** See post on 15/12/2011 for information about Debian 64 bit. It builds fine on Squeeze but not Wheezy. This seems to have to do with the version of mpich2.**

Figuring out how to compile nwchem with mpich support took a little while, but this seems to have worked:

First mpich2 and gfortran need to be installed (since it was not installed on a virgin system there may have been other required packages already installed)
sudo apt-get install mpich2 gfortran

I created a file called myconfig.sh in the nwchem directory, with the following content:

setenv TCGRSH /usr/local/bin/ssh
setenv NWCHEM_TOP /work/nwchem
setenv USE_MPI y
setenv USE_MPIF y
setenv MPI_LOC /usr
setenv MPI_LIB $MPI_LOC/lib
setenv MPI_INCLUDE $MPI_LOC/include/mpich2
setenv LIBMPI "-lfmpich -lmpich"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran >& make.log

do a csh myconfig.sh and you should be good to go.

I then added the following to the end of my ~/.bashrc and sourced it:

export NWCHEM_EXECUTABLE=/work/nwchem/bin/LINUX64/nwchem

Jobs can then be submitted (assuming that mpd is up) by
mpdrun -n 2 nwchem nameofjob.nw

09 January 2011

2. Setting up a cheap-ish ubuntu cluster - the hardware

I've recently  become interested in setting up a small computational cluster for simple QM and MD work. Since it doesn't hurt sharing your experience with others, I'll post the details on this blog.
I'm not a computer/linux/computational chemistry expert - the goal of this project is as much to learn how to go about setting up a cluster, as getting a useful computational tool.

First, the hardware - the idea was to get something fairly cheap, but also reasonably useful. I opted for the following hardware (prices in USD):

30.99    V7 NS1132-N6 10/100/1000Mbps Unmanaged Networking Switch 5 x RJ45 2K MAC Address Table

Each node
39.99    BIOSTAR MCP6P3 AM3 NVIDIA GeForce 6150 / nForce 430 Micro ATX AMD Motherboard
77.00    AMD Athlon II X3 445 Rana 3.1GHz 3 x 512KB L2 Cache Socket AM3 95W Triple-Core Desktop Processor 
2*21.99    Mushkin Enhanced 2GB 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10666) Desktop Memory Model 20-146-744
7.99    NIC Zonet ZEN3301E 10/ 100/ 1000Mbps PCI 32-Bit Network Adapter 1 x RJ45
24.99    APEX TX-381-C Black Steel Micro ATX Tower Computer Case (needs full size ATX PSU)
13.99    LOGISYS Computer PS480D 480W ATX12V Power Supply
3.99    APEVIA CF12S-BK 120mm Case Fan 

I ordered everything from Newegg, and all the parts arrived after three days, as promised.

I already had two SATA harddrives, and two IDE CD ROM drives, in addition to two IDE/PATA cables. The CD ROM drives aren't important, as the mobo bios allows for boot from USB, so you can install your OS that way (at least Ubuntu 10.10).

Assembling the two systems was easy, even though it was the first time I had done anything more complicated than installing a RAM stick or changing a hard drive. I'm not particularly good with my hands, so that really says something.

Here are the steps, in case someone is as useless as I am with hardware:
Preparing the motherboard:
1. The CPU was fitted on the motherboard - being an AM3 socket it was a simple matter of gently dropping the cpu in the socket with the yellow marking on the cpu being aligned with the yellow marking on the mobo.
2. Next the heatsink/fan was fitted. The heatsink arrived with a smooth layer of thermal grease already applied. While it's difficult to see whether the heatsink was in perfect position over the cpu, I did my best and everything went well.
3. The RAM memory was installed. Nothing complicated here.

Preparing the case:
1. The PSU was installed - nothing complicated. Just four screws to attach the PSU to the case.
2. The motherboard panel at the back of the case didn't fit my mobo, so I installed the one which came in the motherboard box. One of the PCI slot covers on the case was removed to make space for the gigabit ethernet card
3. The brass spacers that came with the case were attached to the wall of the case. The spacers are for the mobo to rest on. If you don't install them the mobo won't align with the openings at the back of the case, so there's little risk that you'll forget to do this.
4. A CD drive (IDE) and a harddrive (SATA) were installed, but not connected.

1. The motherboard was attached to the case by resting it on the brass spacers and aligning the holes in the mobo, then attaching the mobo with screws.
2. All the cables connected to the case were clearly labelled, as were the corresponding connections on the motherboard, so it was just a matter of matching one to the other.
3. The PSU cables were fairly simple to connect two - two cables were attached to the corresponding connections on the mobo (just going by shape), the sata power cable was connected to the HDD and a molex connector was connected to the IDE CD ROM drive.
4. The sata cable that came with the case was used to connect the motherboard with the harddrive. I had a couple of IDE cables around, and used it to connect the CD ROM drive to the motherboard.  It took two attempts to get the IDE thingy right as I first attached the cable the wrong way round - for an IDE cable with three plugs (one on each end, one slightly offset from the middle of the cable) you want to connect the end with the 'middle' connector closer to it to the CD ROM, and the other end to the MOBO. Makes sense, but getting it right the first time would save you a few minutes. Of course, an easier way of getting around this is probably by setting the jumper to cable-select.

One system was installed by booting from a Ubuntu 10.10 64 CD, and the other by booting from a USB stick prepared using usb-creator-gtk. I could've settled on minimal/server installs instead of full Ubuntu Desktop installs, but as I 1) will later modify grub to boot to terminal instead of starting Gnome, 2) don't have space contraints and 3) want to be able to use the computers as back-up workstations I opted for full installs.

The systems were updated after the install.