Monthly Archives: July 2014

GTX570 for the Mac Pro

The Mac Pro 4,1 has been upgraded with a used GTX570 which I brought for $130. A nice little upgrade that hopefully will do something for Perfect Photo Suite 8 which was the main cause for this upgrade. Apparently Perfect Photo Suite 8 relies on OpenGL. The stock GT120 are getting really old so the GTX570 would be a significant upgrade.

Prior to getting the GTX570, I had to buy 2 mini to standard 6 pin PCIe power cables so that I can power the GTX570. The Mac Pro mainboard has 2 headers for the mini 6 pin PCIe power cable which terminates to standard size versions. This is needed by the GTX570 for power. The cables took a while to ship (I got it from eBay) and they packed only one cable initially. After that confusion was cleared, it took another while to ship the other cable. Finally with the renovations at home, things were in a mess and I lost one of the cables. After finally locating the cable a couple of days back, I transplanted the GTX670 from the Windows box to the Mac Pro and lo and behold, it works right out of the box. No driver installation needed.

Prior to getting the GTX570, I considered the AMD 5870 Mac Edition but it was really expensive. Googled and found the following forum thread:

http://forums.macrumors.com/showthread.php?t=1440150

The thread shows that selected standard NVIDIA cards would work out of the box and this is certainly true in the case of the GTX670 and GTX570. The only difference I see is the lack of the white screen during boot up.

Once I knew that the GTX670 works, I got a GTX570 off the local forum since I just need a reasonable modern graphics card and was not willing to spend >700 on a GTX780. Had I got the GTX780, I would have used it in the Windows box since I game on that one. The GTX670 would then go to the Mac Pro. After getting a GTX570 at a low cost, perhaps a used GTX670 for SLI would be a better idea in the future.

All in all, a good experience which really shows that the Mac Pro still has a lot of life in it still.

Genome size

For computation of genome coverage, a bed file containing the sizes of the chromosomes is very useful. This can be done easily on the command line as follows:

# get the hg19 sizes from UCSC
wget "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz"

# gunzip and pipe to awk to process the file to a standard bed file
gunzip -c chromInfo.txt.gz | awk -F $'\t' 'BEGIN{OFS=FS}{print $1, 0, $2}' > hg19.bed

Coverage of some features in another BED file can then be computed using bedtools as such:

bedtools coverage -a some_features.bed -b hg19.bed

This will produce a output showing the coverage on a per chromosome basis.

Kids at the playground

The kids were at a playground at Bedok and I took the opportunity to shoot some pictures of them using the GX7 and 20mm 1.7.

Shooting with a fast prime is always nice. The GX7 and the pancake prime makes for a very small package which is great for traveling.