A few useful Windows HPC commands

0. Set Default scheduler

set CCP_SCHEDULER=headnode_name

1. clusrun

One can run the following command from his desktop to setup compute node environments

clusrun /user:domain\username dir

clusrun /user:domain\username xcopy \\headnode_name\dir .

clusrun /user:domain\username setx PATH "somepath"

2. job

job list /scheduler:headnode_name

3. node

node list /scheduler:headnode_name

5. cluscfg

cluscfg setcreds

More details are available at http://technet.microsoft.com/en-us/library/cc972841(WS.10).aspx

Imporve serialize() in R for windows

serialize() function of R is very slow in Windows. My observation is that calling realloc is the bottle neck. The workaround can be replacing realloc with Rm_realloc in $R_HOME/src/main/serialize.c. More specifically, I have updated as follows:

1. In function, resize_buffer(...), replace

mb->buf = realloc(mb->buf, newsize);

with

mb->buf = Rm_realloc(mb->buf, newsize);

2. In function, free_mem_buffer(...), replace

free(buf);

with

Rm_free(buf);

Directions for compiling R in Windows are in http://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-can-I-compile-R-from-source_003f

The following is a short result running on my Windows 7 desktop:

The original:

> system.time(serialize(matrix(0, 1000, 1000), NULL))

user system elapsed

5.74 4.39 10.15

> system.time(serialize(matrix(0, 2000, 2000), NULL))

user system elapsed

85.40 74.80 161.62

After updating:

> system.time(serialize(matrix(0, 1000, 1000), NULL))

user system elapsed

0.78 0.30 1.10

> system.time(serialize(matrix(0, 2000, 2000), NULL))

user system elapsed

6.21 4.13 10.54