Installing GMAC

GMAC is a user-level library that implements an Asymmetric Distributed Shared Memory model to be used by CUDA programs. An ADSM model allows CPU code to access data hosted in accelerator (GPU) memory.

GMAC is being developed by the Operating System Group at the Universitat Politecnica de Catalunya and the IMPACT Research Group at theUniversity of Illinois

 

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To install gmac,

1. Download the latest version of gmac to date: gmac-0.0.10.tar.gz

2. Unzip gmac-0.0.10.tar.gz using the following command

gunzip gmac-0.0.10.tar.gz
 tar -xvf gmac-0.0.10.tar

3. Go inside the directory gmac-0.0.10 and make another directory build to separate the installation files from the source.

cd gmac-0.0.10
 mkdir build

4. Go inside the directory build and run configuration file

cd build
 ../configure

5. Install using make all install command

sudo make all install

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I am installing gmac on a 32 bit UNIX machine with gcc 4.3 and CUDA 3.0.

After installing from the Makefile I encountered the following error

/usr/bin/ld: cannot find -lcuda
collect2: ld returned 1 exit status
make[5]: *** [libgmac.la] Error 1
make[5]: Leaving directory `/home/imacbuntu/Projects/gmac-0.0.10/build/
src/gmac'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/imacbuntu/Projects/gmac-0.0.10/build/
src/gmac'
make[3]: *** [all] Error 2
make[3]: Leaving directory `/home/imacbuntu/Projects/gmac-0.0.10/build/
src/gmac'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/imacbuntu/Projects/gmac-0.0.10/build/
src'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/home/imacbuntu/Projects/gmac-0.0.10/build/
src'
make: *** [all-recursive] Error 1

 

The error has something to do with the library of cuda,

when I tried to link the libcuda.so in /usr/lib by performing the following command, installation of gmac became successful.

sudo ln -s /usr/lib/nvidia-current/libcuda.so /usr/lib/libcuda.so



Sources: http://code.google.com/p/adsm/

How to reset the motherboard

Resetting the BIOS or the motherboard may fix CHECKSUM ERROR.

To do this, try resetting the jumper on the motherboard.

This will change the BIOS setup to factory setting.

Please see the following description for more information.

Source: http://patkay.hubpages.com/hub/the-motherboard-components#

Jumper pins

Jumpers are small pins on the board with plastic or metal devices that go over the pins. This device is called a bridge or a jumper cap. When the bridge is connected to any two pins via a shorting link, it completes the circuit and a certain configuration has been achieved.

Jumper cap

A metal bridge that closes an electrical circuit. Typically, a jumper consists of a plastic plug that fits over a pair of protruding pins. Jumpers are sometimes used to configure expansion boards. By placing a jumper plug over a different set of pins, you can change a board’s parameters.

Installing Projection Toolkit for Motif Finding

If you are using a linux terminal, perform the following to install projection toolkit from source file.

1. Download the source files from the terminal by using wget command. It will download the file to the present working directory

$ wget http://www.cse.wustl.edu/~jbuhler/pgt/projection-toolkit-0.42.tar.bz2

2. Unzip the tar bz2 by typing the following in the command line

$ bzip2 projection-toolkit-0.42.tar.bz2

$ tar -xxvf projection-toolkit-0.42.tar

3. Add the following line to shared-src/{alignalgos.cc, annoio.cc, parseline.cc, seqio.cc}

#include<stdlib.h>
#include<stdio.h>
#include<string.h>
4. For 64-bit architectures, comment out the line with ARCH in Makeconfig file.

#ARCH = -march=pentium3 -fomit-frame-pointer

5. Run make specifying 64-bit architecture.
make MACHINE_TYPE=i686-m64
If installation is successful, executable files will appear in the topmost level of projection-toolkit-0.42 directory.
For more information read the README file in projection-toolkit-0.42/doc/