|Posted on May 16, 2011 at 5:38 PM|
On April I moved to Donostia to start a postdoctoral stay in the group of Prof. Jesús Ugalde. I'm employed in the Donostia International Physics Center (DIPC) and work in the Faculty of Chemistry in the Euskal Herriko Unibersitatea (EHU). The group is about 15 people and they work on a wide variety of research subjects which, to my convenience, includes harmonium. My experience this first month could not be better. People in the group is very nice and the city, Donostia, is charming. I will stay in Donostia until the of November, then I will move back to Girona.
I'm hosted in the Talent House a residence for postdoctoral researchers that has been recently inaugurated. This residence is just an example of the investment that the city (and the Basque Country) is doing on research. Some time ago Catalunya invested on research and started the program ICREA, whose results are showing in the most competitive european research projects. Spain was awarded 23 grants in the last call of the Starting Grant, 9 of which were to Catalan institutions and 3 to Basque research centers. More recently the Basque Country started the ikerbasque program, quite similar to ICREA. Nowadays, ICREA program has reduced its budget (initially ICREA hired both senior and junior researchers, lately only seniors) while the Basque Country is investing more on research. I believe it's matter of time for the Basque Country to catch up to Catalunya.
|Posted on May 14, 2011 at 8:03 AM|
About a year ago I posted an entry in this blog discussing peer-review process. Today, via twitter I received an article from the editors of the Journal of the American Chemical Society (JACS) to draw our attention on "the moral responsibilities of our referees". Basically the article is critical with those researchers that refuse to write reviews or write a late report that it is of no use. After this article I get the impression JACS editors are mainly concerned about getting reports and getting them on time.
I was startled to see no reference to the quality of the report. They mention all sorts of malpractices (not answering, refusing to report, consulting othe rscientists without editor's consent, removing oneself for long periods from the list of active referees) but they do not mention about writing bad scientific reports. Maybe they do not want to put the researcher's competence into question. Fair enough; but then, they shouldn't mention about these other malpractices either; they all concern the 'moral responsibility' of the reviewers.
The editors should put as much effort on getting good-quality reports as they do on getting quick reports. Lousy reports are potentially more harmful than no report at all. Lousy reports often refuse or accept the paper directly, without much explanation of why the paper merits such qualification. Lousy reports make lousy papers published. If the author feels mistreated, he may appeal. However, experience indicates that his success will mostly depend on his relationship with the editor, rather than on the quality of his paper.
Let me mention a recent episode I experienced while reviewing for JPCA (ACS) and PCCP (RSC). I received a paper to review from these journals and they gave a deadline to respond (between two-three weeks). I read both papers and, in both cases, when I was about to write the report I received e-mail from the editor saying that my report was not longer necessary. In both cases it happened before the deadline. I was pissed. I get the impression editors contact more referees than necessary and then they discard those that come latest. Obviously, such practice increases the demand of referees.
Scientific publishing is business. Let's not forget it. Apparently any strategy is good to increase the publication speed. And if such strategy uses reviewer's time, it does not bear any cost to the journal.
If editors want ((good-quality)) quick reports, they should acknowledge referee's task. It does not make any difference how many papers I review every year. At most I get a Xmas card, lately not even that. I am not sure which should be the mechanism to reward the reviewers, but something has to be done.
I advocated here for responsible reviewer performance. My idea is that anyone should cover the demand of reports his papers generate; I guess this is (morally) responsible. But I also claim for editors' moral responsibility to acknowledge the referee's task and appreciate their time.
|Posted on May 9, 2011 at 6:21 PM|
My time in Szczecin came to an end. After two short years filled with all sort of adventures I'm moving on. My next destination is Donostia, in the Basque Country... but that will be the issue of a coming post. In the following lines I will sum up my experience in Poland.
The group was very small but people were nice to me (Jerzy, Jacek, Marcin, Ewa,Stan and lately Joanna). Scientifically, I have no complaints. I already knew Jerzy, both the guy and the scientist and we understood each other quite well. He is the most knowledgeable scientist I have ever met, and probably I will ever meet. I have learnt a great deal of things from him, and together we have put the basis (algorithm and software) for the study of few-electron harmonium systems. I had also time to learn on my own some basic guidelines to program in parallel (mostly with MPI protocol), which I used to parallelize a few codes of mine. I familiarized myself with literature in the field and got a couple of ideas, which little by little turned into a four-year research project to(hopefully) develop at some point in the coming years. The number of papers published on the main research subject of this postdoc is not large (three so far), but this is mostly because the development of the code/algorithm toke most of my time, the calculations were time consuming and they needed large computational resources that were not easy to obtain. We are actually still looking for resources to finish four-electron harmonium calculations (ideas welcome!). Therefore, some more publications should appear in the coming years. Besides, I also dedicated a not-so-small fraction of my (free) time to work on other research projects because, no matter how much I learn, no papers is no future. The competition is really high. I started collaborations with Prof. Kallol Ray (computational calculations), Prof. István Mayer (decomposition of total spin angular momentum), Prof. Mihai Putz (conceptual DFT), Prof. Gabriel Merino (aromaticity) and my former group in Girona (Prof. Solà's). These collaborations and the last papers from my postdoctoral stay in Denmark with Prof. Ove Christiansen provided the gross publication record during these two years of postdoc.
My only problem on my stay in Szczecin was the university administration. Unfortunately the university did not have (and it doesn't) the adequate infrastructure to hold a Marie Curie fellow (IEF). People who were supposed to take care of my fellowship did not know anything about it and sometimes simply noone took responsibility for it. Everytime there was an issue with my grant it was a nightmare for them... and for me. Someway, somehow (Polska!) it went through, but not without much time and effort from my side. Here I should mention Jacek who did not benefit from this fellowship (and it was not his duty) and carried on his shoulders the paperwork and problems related with the IEF. What is more, he bore my complaints with cheerful equanimity. Without him I would have surely packed and left after the second month. Don't get me wrong, I had an ample office, broadcast connection and nice atmosphere to work (all that a theoretical chemist needs), but every little paper work was a big deal and lots of mess.
On the personal side I had a great time in Szczecin, mostly because of Jacek (yep, the same guy!) and Jadwiga. They were my neighbors and my friends; we shared dinners, Sunday lunches, bottles of wine and Easter parties. Basically any excuse was good to meet. They also helped me with many issues of my apartment that I could not take care by myself because of the language barrier. There are not enough words to acknowledge what they did for me.
All in all, I do not regret a single day I spent in Szczecin. It was a worthwhile experience that I will never forget.
Last dinner in Zbójnicka. From left to right: Jerzy, Jacek, my long-hair-no-shaved me and Marcin.
|Posted on April 13, 2011 at 12:11 PM|
My last month in Poland I organized a mixture of vacation and lab-visiting. I had the opportunity to give talks on the 'Vibrational Auto-adjunting theory' and 'The Electron Localization Function' (see papers 26 and 36) in the Wroclaw University of Technology and the Technical University of Lodz respectively. I was invited to Wroclaw by Robert Zalesny who was a formidable host. In Lodz I was visiting Kasia Pernal and staying at her place. I was impressed by the size of the group in Wroclaw. Kasia's group just started but it is already producing very interesting papers.
On my vacation with Anna we visited Wieliczka, Krákow and Zakopane. Hard to decide which one was best. Krákow is probably my favourite city in Poland (with permission of Torun). In Zakopane we enjoyed the folklore in Chata Zbójnicka. The salt mine in Wielczka is simply impressive, worth a visit. I had almost no time to visit Wroclaw but I was already familar with this charming city. My visit in Lodz was brief, but apparently there is no much to see there, excepting for the Manufaktura (see photo).
|Posted on October 27, 2010 at 6:51 PM|
This week I spent a few days in Torun invited by Prof. Jacek Kobus. I gave a seminar about the harmonium project. I leave the talk here. I love the mistic atmosphere of the old city, its people and the food. Torun is certainly one of my favorite cities in Poland. The university is very nice, and it is growing with the help of EU funds. A quantum optics center linked to the university is just being build.
|Posted on October 26, 2010 at 9:29 AM|
The last call for BSC granted us with 70,000h to run our code. So we will be able to test the efficiency of the parallelization of our code and also to obtain some results for four-electron harmonium. An unfortunate event (the workstation in Szczecin halted) allowed me to test the performance on 16 cores. The results are very promising for the symmetry-related part of the code, yielding an efficency of 89% in 8 cores. There are some magic numbers of processors which yield the best performances. They correspond to submultiples of 64: 2, 4, 8 and 16. No surprise here, an even distribution of tasks maximizes the peformance. Obviously this is related to the way processors are distributed; there is a nice linear trend which relates the number of tasks (out of 64) per core with the computational task.
Maximum number of tasks assigned to each processor vs. time (s).
The only warning shows for the 16-processor job, which 'only' yields a performance of 76%. But I'm not much worried about that because using 16-processors we are saturating the machine (thus the job competes with system processes) and, in addition, one should notice the task split into 16 processors only takes 15 minutes (actually the same parallelized routine is called 10 times during these 15 minutes, therefore the performance is tested on a 1.5 minutes run, and delay accumulates ten times), which is not a long enough time to obtain reliable data.
|Posted on October 17, 2010 at 9:49 AM|
Last week I finished the implementation of the MPI-version of the double loop in the sigma vector calculation in Knowles program. The performance of the parallelization is very good, with an efficiency of parallelization above 85%. And most interestingly, it looks like the performance will hold with larger number of processors because the computational time decreases linearly with the number of processors. The maximum number of jobs allowed for this part of the code is 64, corresponding to the double loop over the number of irreducible representations (eight) of D2h group.
procs t(s) cpus effic
6 2345 5.14 86
5 2788 4.33 87
4 3200 3.77 94
3 4522 2.67 89
2 6720 1.79 90
1 12060 1.00 100
These calculations should be taken as a guide, because they were performed in a workstation with other processors running at the same time. If eventually I get an empty workstation to use, I would provide the new parallelization data. However, I don't expect major differences.
|Posted on September 24, 2010 at 11:04 AM|
As I mentioned few months ago we want to produce benchmark calculations for few-electron harmonium. The idea is to use this information in the calibration of quantum chemical methods, and specially we have in mind the design of a new functional using these data. To this aim, we developed a method to produce highly accurate results for few-electron harmonium. The method uses an extrapolation scheme based on few FCI calculations. Since these calculations for more than three electrons are prohibitive, we are developing an MPI version of the code. This post is about such possibility and a few benchmark results we have obtained so far.
In order for the extrapolation scheme to work we must use a particular basis set. There are many basis sets adequate for extrapolation schemes, but these basis are optimized for molecular systems and they are not so good for harmonium. Our basis set consists of even temperated gaussian functions, the exponents of which (alpha, beta) are optimized for each calculation using the simplex method. The simplex method shrinks and shift along a grid of nine points, and therefore we can expect few calculations that can run simultaneously. We always start with 9 calculations needed and every time we shrink the grid we need additional eight calculations, if we shift, between 3-5 calculations are needed for the next step. Therefore, in this first step we may use between 3-9 processors. This part is trivial to parallelize (it's an embarrassingly parallel problem).
In order to perform the FCI calculation we use a modified version of the Peter Knowles' code (CPL 1989). This code uses D2h symmetry to perform Davidson iterations over a FCI matrix constructed from Slater determinants. Since the program uses symmetry, it can be parallelized through the different irreducible representations of D2h point group. Namely, the calculation of the sigma vector -which involves a double loop over the eight irreducible representations- can be parallelized. We may thus use up to 64 processors in this part of the program.
2) The Sigma vector.
Each of these 64 tasks running in parallel contain a main procedure that takes most of time: the calculation of the sigma vector. The calculation of the sigma vector involves a large matrix multiplication. We can also split this last task among different processors (as simple as letting one processor handle one column at a time).
Therefore, altogether we can expect our code to parallelize very well among 192N to 576N processors. This factor N is the number of processors among which we could split our matrix multiplication. We have requested by third time [sic] computational time in the Barcelona Supercomputer Center (BSC), in there the maximum number of processors we can use in one parallel job is 1024. So this means we should prove the MPI subroutine for matrix multiplication parallelizes well for 2-5 processors. Let me give you some numbers of parallelization (these are lower bounds to the actual performance because few processes are running in the same workstation):
1 proc 3 proc* 5 proc*
total time (s) 26,689 10,077 (2.6) 6,737 (4.0)
largest multiplication (s) 1,996.85 670.97 (3.0) 403.32 (5.0)
* The numbers in brackets correspond to the number of processors used (ideally they should correspond to the numbers of processors requested).
These numbers prove that an efficient parallelization among up to thousand processors is possible with our modified FCI code. Nowadays I have implemented the matrix multiplication in parallel and I'm working in parallelization among the different irreducible representations (I expect to have it ready in less than two weeks). The parallelization of the optimization process is quite trivial and can be done in a few hours.
|Posted on August 2, 2010 at 7:01 PM|
It's summer time, and I will have a short break for two weeks, starting this Friday evening. I plan to spend one week by the seaside. I will bring some stuff to read to the coast, but I will be unplugged and mostly resting and meeting friends. The second week I will be taking it easy but available from time to time in the net.
Have a nice vacation!
|Posted on July 7, 2010 at 10:17 AM|
Last but not least, I'm attending the Girona seminar. The ninth edition of the binnual conference organized in Girona by the IQC (my former lab) dedicated to Ramon Carbó-Dorca 70th birthday. This year organizers managed to bring an exhaustive list of highly recognized experts, the longest I recall in Girona. I have had the opportunity to give a small talk on three-electron harmonium.
In 'el Celler': Jadwiga and Jacek Styszynski, Josep Roca, Jerzy Cioslowski, my brother Xevi and me.