Dear Ibrahim,
This page may help: www.pqs-chem.com.
Bes= t Regards.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
= Obafemi Awolowo University,
Ile-Ife,= Osun State.
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091

On Monday, 9 December 2013, 15:55, Daniel Jana dfjana . gmail.= com <owner-chemistry_+_ccl.net> wrote:

Sent to CCL by: Daniel Jana [dfjana_-_gmail.com]Hello,

Strategy 1 - I see no problem with having multiple users us= ing the
same computer. Of course, physically it's hard... you tend to only
have one = keyboard and screen after all. However, once you have the
computers on t= he network, nothing prevents other users from connecting
(I assume we ar= e talking about Linux workstations) via SSH and
launching calculations. = Through a combination of job priority and
appropriate choice of the numb= er of cores, the machine can be used for
regular work (checking journals= on the web, reading/writing papers,
the occasional video on youtube bec= ause no one works 100% of the time)
while running jobs.
The easiest w= ay to manage the software will be having a NFS-shared
partition with all= the software installed. This means you only install
the software in one= place, rather than locally in every machine.
In this scenario, users ty= pically check for available workstations and
run their jobs directly on = the machines. You can always go the
extra-mile and install a scheduler so they can submit jobs to the
queue and it runs on the first= available machine. But that may be too
much to learn in the beginning.<= br>
Strategy 2 - Obviously having a cluster is the ideal solution, but I= 'm
not sure with that budget you'll go far. Perhaps you buy computers> from a regular shop and not rack-ready hardware, making it a bit
c= heaper). You will still have a lot of computers in the same room
produci= ng heat. You have to at least consider the possibility that
part of that= money will go to buying and installing AC. If you go with
strategy 1 yo= u probably will have the students spread over several
rooms so the probl= em becomes less obvious. And buying a rack-ready
cluster will also mean = buying a rack. With such a small budget it may
end up not being a neglig= ible part of your budget.
Concerning Amber/Gaussian... those two codes h= ave different
capabilities when it comes to scaling to many cores. My personal
feeling is Gaussian scales poorly beyond 8 cores and= poorly over more
than one machine. Amber, on the other hand, should be = more or less
linearly scaling for at least a few hundred cores. This mea= ns that if
you plan to have a cluster for Gaussian there's not much of a= need for
Infiniband, while for Amber it does make sense (because runnin= g it
over Ethernet does impact the performance substantially. Of course,=
with a total budget of 40 kUSD, talking about Infiniband is probably a<= br>bit stupid.

I'd say in the beginning strategy 1 makes more sense.= You still need
computers for the students anyway... no point having a c= luster if
users can't connect to it. You can also start learning slowly = the
tools needed to have a cluster (e.g. learning NFS in the beginning t= o
share the software; later on installing NIS to manage the users
cen= trally, rather than having to install all users on all
workstations; later on installing a scheduler so that jobs can beautomatically submitted to remote machines). It's true that it's not
t= rivial to manage one, so taking baby steps is probably the best way
to g= o at it. When you feel more comfortable with it, perhaps even
having one= or two students capable of dealing with all the needed
tools that make = a cluster, perhaps you could then think about
acquiring a cluster, poten= tially with a few other groups so you could
make an investment giving yo= u a cluster with 30 or 40 nodes.

When it comes to software: I would = avoid as much purchasing
non-scientific software. Why spend money on an = OS, when Linux
(provided you and your students have either the skills or= the time to
learn them) costs nothing and is probably the best solution= ? Once your
students are accustomed to the shell, they can start working= on
scripts that make their life easier (e.g. by parsing the output files
and extracting only the relevant bits, rather than having = to do it all
by hand). Linux and related tools will cover most of your n= eeds (even
if you go for a cluster, NFS, DHCP, SSH, NIS, are all readily=
available and there's plenty of information on how to get them to
wo= rk). And if you are anyway considering a cluster, chances are you'll
nee= d to learn Linux anyway. At least for the cluster, you need a
scheduler = to manage the jobs of the users (although, as I mentioned
earlier, it ma= y even make sense with the workstations). Lately I've
been inclined to u= se SLURM. Torque feels a bit abandoned, SGE split
into so many things af= ter Sun got bought by Oracle that I don't even
know which version to ins= tall. I could name a few other but some of
the ones I've tried just felt= too bad to be put into production. SLURM
is a young project, it has som= e quirks, but it seems a good bet for
the near future. Compilers: in the beginning you can certainly work
with GNU compilers (gcc, gfortr= an, ...), coming with Linux. Most of
the codes you need to compile will = work with those. You'll definitely
need to install BLAS and LAPACK. Perh= aps they will be available from
the Linux distribution you choose. But i= t would be best to compile
them locally, for optimal performance. FFTW 2= and 3 will also be
important, but you'll figure that out quickly. Howev= er, on the long
run, consider purchasing Intel compilers and MKL. The co= des compiled
with those are often faster than those compiled with GNU co= mpilers.
With a limited number of machines, efficiency may be the best u= pgrade
you can get.

As for vendors, I feel I cannot give you a go= od answer. Certainly the
best vendor in Egypt is not the same as here (r= ead best in whatever
way you want, from cheapest to the one giving the b= est costumer
service).

I hope this helps,
Daniel

PS - Please consider a backup solution. You may go= with strategy 1 for
now, but it serves no purpose to have all those com= puters and risk
losing months of work because a hard drive died. Conside= r buying a
machine, with several disks and several times the capacity of= the
individual computers and automating backups of the workstations. It=
can even be the machine where you install the software, to reduce
co= sts. Bonus points if you manage to have it in a separate location
(e.g. = a server room on the other side of the campus). Like this you
avoid losi= ng the backups and the workstations when a fire burns your
lab or when s= omeone steals some computers overnight. It may seem that
you can think a= bout this later, but from personal experience and
anecdotal evidence, pe= ople only think about backups when it's too
late, when you already need = them.

On 8 December 2013 20:55, Mahmoud A. A. Ibrahim
m.ibrahim[A]compchem.net <owner-chemistry%a%ccl.net> wrot= e:
>
> Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim^compc= hem.net]
> Dear Colleagues
> We ask you kindly to share your ex= perience with us.
> Nowadays, we are establishing a new computational= chemistry lab and aiming to
> purchase some hardware.
> The bu= dget is not high. It is around 40,000$.
> We have two strategies:
= > 1- Purchase good workstations with the available budget. The problem i= s that
> only one user will use the workstation, i.e. we need a works= tation per each
> student. If there is any way to make many users to = use the same workstation
> at the same time, please share your knowle= dge with us and let us know.
> 2- Purchase a small HPC which can be u= pgraded in the near future (just add
> more processors and storage di= sks). I prefer this strategy which makes us
> able to increase our facilities in the future very easily without getting red
> off t= he old ones. But, we don't have a professional technicians herein at the> current time, and our colleagues say that it is not easy to manage a = small
> HPC to handle your jobs.
> We need your experience and = let us know if you were us which one you would
> purchase (workstatio= ns or small HPC).
> It would be nice from you if you let us know what= all hardware and software
> you need to purchase starting from opera= ting system upto the software
> responsible for handling the jobs and= compilers. As well in case of purchase
> HPC/workstations, which com= pany you would recommend.
> For your information, we are aiming to ru= n Gaussian calculations and AMBER
> simulations at the current time.<= br>> Finally, we thank you deeply in advance for your support.
> S= incerely;
> M. Ibrahim
> P.S. we read many posts on CCL regarding the hardware but because of the fast
> growing up of techn= ology we are afraid we missed something around. We do
> apologize for= any inconvenience caused.
> --
> Mahmoud A. A. Ibrahim
>= Editor, Journal of Organic and Biomolecular Simulations (JOBS), Science> Publications
> Group Leader, CompChem Lab, Chemistry Department= ,
> Faculty of Science, Minia University, Minia 61519, Egypt.
>= Email: m.ibrahim()compchem.net
> &= nbsp; m.ibrahim()mu.edu.eg
> Website: www.compchem.net>
>

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