Sunday, November 9, 2014

Fedora 20 update to kernel 3.17.2-200 and VMWare Workstation

Well, here we go again. After recent update which brought kernel 3.17 to Fedora 20, VMWare Workstation 10.0.4 had problems with kernel modules. Luckily, after some short googling I found a solution. That solution works. There are two things that might confuse you though:

  1. After cd command and before for loop you have to switch to root account (that is indicated by prompt sign change from $ to #).
  2. The substring kernel-version in patch command should be replaced with a string "3.17". That is actually the name you gave to a file while executing curl command at the beginning of the process.
Anyway, that's it.

Wednesday, September 24, 2014

Anonymous paper reviews and threat of a legal action

I just stumbled on a news story in which scientist claims that his career was severely damaged by anonymous comments on some of his works published on PubPeer. This is very interesting story to follow for several reasons.

For a start, PubPeer is a site for a post publication review. I strongly support such a practice because I believe that everything has to be scrutinized and tested, and it helps authors who can get the best possible feedback, but also helps society in general, too because there is ever increasing problem with scientific ethic. As a side note, I was, and I'm still a big proponent of doing review process in public. That, in my opinion, significantly increases transparency. Anyway, PubPeer fulfils my wishes, but unfortunately for me, it is only concerned with papers from medicine, chemistry and related fields, not from computer science.

In this particular case, the problem is that the author was offered a job on the University of Mississippi, with quite a large annual salary, and for that purpose he quitted his current job. University then revoked the offer and so he lost both the new job, and his current job. Now, he claims that the reason for this are some anonymous negative comments on PubPeer and threatens with a lawsuit asking for identities of those who made those negative claims.

While, as I said, it is very good to have such a site, it doesn't mean that everything should be allowed, more specifically:
  1. Any claims made have to be justified. Unfortunately, anonymity also allows people to make damaging or unjustified claims by being certain that there will be no repercussions.
  2. Unfortunately, negative claim even if not justified casts doubts, so that might be a problem.
  3. In this particular case it is also unknown why the author didn't respond to presented claims about problems in his paper. PubPeer claims they invite first and last author to comment on comments.
  4. Finally, no one should take lightly claims about some paper being invalid, not good, etc. In this particular case, I hope that University of Mississippi verified negative claims and that they didn't take lightly what some anonymous commenters said.
In any case, we'll see what will happen with this particular case.

Saturday, August 23, 2014

Memory access latencies

Once, I saw a table in which all the memory latencies are scaled in such a way that CPU cycle is defined to be 1 second, and then L1 cache latency is several seconds, L2 cache even more, and so on up to SCSI commands timeout and system reboot. This was very interesting because I have much better developed sense for seconds and higher time units that for nanoseconds, microseconds, etc. Few days ago I remembered that table and I wanted to see it again, but couldn't find it.  This was from some book I couldn't remember the name. So, I started to google for it, and finally, after an hour or so of googling, I managed to find this picture. It turns out that this was from the book Systems performance written by Brendan Gregg. So, I decided to replicate it here for a future reference:

Table 2.2: Example Time Scale of System Latencies
Event Latency Scaled
1 CPU Cycle 0.3 ns 1 s
Level 1 cache access 0.9 ns 3 s
Level 2 cache access 2.8 ns 9 s
Level 3 cache access 12.9 ns 43 s
Main memory access (DRAM, from CPU) 120 ns 6 min
Solid-state disk I/O (flash memory) 50 - 150 us 2-6 days
Rotational disk I/O 1-10 ms 1-12 months
Internet: San Francisco to New York 40 ms 4 years
Internet: San Francisco to United Kingdom 81 ms 8 years
Internet: San Francisco to Australia 183 ms 19 years
TCP packet retransmit 1-3 s 105-317 years
OS virtualization system reboot 4 s 423 years
SCSI command timeout 30 s 3 millennia
Hardware (HW) virtualization system reboot 40 s 4 millennia
Physical system reboot 5 min 32 millennia

It's actually impressive how fast CPU is with respect to other components. It is also very good argument for multitasking, i.e. assigning CPU to some other task while waiting for, e.g. disk, or something from the network.

One additional impressive thing is written below the table in the book. Namely, if you multiply CPU cycle with speed of light (c) you can see that the light can travel only 0.5m while CPU does one instruction. That's really impressive. :)

That's it for this post. For the end, while I was searching for this table, I stumbled on some additional interesting links:

About Me

scientist, consultant, security specialist, networking guy, system administrator, philosopher ;)