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Dear Chang,
some time back people would benefit from the computational time (or
e.g. data collection time) to get a coffee, lean back and think about
what was going on - this was often very efficient and not rarely more
effective than the false perception of computers being able to think
for oneself ;-)
You can also parallelise programs yourself by means of shell scripting
for example if you want to test several parameter settings. The
following e.g. is a script to keep an 8-core computer busy for a
couple of days even if shelxl were not parallelised:
#!/bin/bash
for i in $(seq -w 99); do
test -f kcross_set${i}1.lst || nohup shelxl kcross_set${i}1 -t1 >
/dev/null & pid1=$!
test -f kcross_set${i}2.lst || nohup shelxl kcross_set${i}2 -t1 >
/dev/null & pid2=$!
test -f kcross_set${i}3.lst || nohup shelxl kcross_set${i}3 -t1 >
/dev/null & pid3=$!
test -f kcross_set${i}4.lst || nohup shelxl kcross_set${i}4 -t1 >
/dev/null & pid4=$!
test -f kcross_set${i}5.lst || nohup shelxl kcross_set${i}5 -t1 >
/dev/null & pid5=$!
test -f kcross_set${i}6.lst || nohup shelxl kcross_set${i}6 -t1 >
/dev/null & pid6=$!
test -f kcross_set${i}6.lst || nohup shelxl kcross_set${i}7 -t1 >
/dev/null & pid7=$!
wait $pid1
wait $pid2
wait $pid3
wait $pid4
wait $pid5
wait $pid6
wait $pid7
done
Be careful with such scripts, though, because you may easily stall the
computer busy with swapping ;-)
Best,
Tim
On 12/17/2013 01:56 PM, Chang Qing wrote:
> Dear Tim
>
> Yes, it is just my impression. I don't know how to test it. As now
> most of computers have multi-core CPU, I really hope CCP4 programs
> can be paralleled. Thank you so much for answering my questions.
>
> All my best
>
> Chang
>
>
> 2013/12/17 Tim Gruene <[email protected]>
>
> Dear Chang,
>
> Without being aware of the various means to parallelise a computer
> program I would be surprised if refmac5 was parallelised for
> MacOSX but not for Linux, although I am sure Garib would correct me
> if I was wrong. Maybe you only have the impression that refmac5
> uses several cores on MacOSX?
>
> Regards, Tim
>
> On 12/17/2013 01:05 PM, Chang Qing wrote:
>>>> Thanks so much. XDS program is a very good example for
>>>> multi-core cpu processing. I love it. I also have a macbook.
>>>> Though a notebook, it often runs CCP4 program more quickly
>>>> than on desktop computer. The programs, for example refmac5,
>>>> seem to use multi-core on OSX and single core on linux. Is
>>>> that mean CCP4 runs more efficiently on OSX than linux?
>>>>
>>>> Best
>>>>
>>>> Chang
>>>>
>>>>
>>>> 2013/12/17 Tim Gruene <[email protected]>
>>>>
>>>> Dear Chang,
>>>>
>>>> this is hardly a matter of configuration but a question of
>>>> programming (meaning you cannot change it unless you modify
>>>> the source code and recompile). You can run a program of
>>>> which you know it is parallelised, e.g. XDS, shelxl, shelxd,
>>>> and check with the command 'top' that your %CPU is about
>>>> 400%.
>>>>
>>>> You can also get the program i7z for more detailed
>>>> information about the status of your CPUs.
>>>>
>>>> Phaser is parallelised, but I dare say it is rather an
>>>> exception within the ccp4 suite.
>>>>
>>>> So all you can do is encourage the developers of
>>>> cpu-demanding programs to spend time on parallelising their
>>>> code - XDS is one of the most impressive examples of how much
>>>> this can be worth in the context of acceptance and
>>>> propagation.
>>>>
>>>> Best, Tim
>>>>
>>>> On 12/17/2013 02:51 AM, Chang Qing wrote:
>>>>>>> Dear all
>>>>>>>
>>>>>>> I just installed CCP4 6.4 on Ubuntu 12.1. The program
>>>>>>> can work. I found it just used 1 processor instead of
>>>>>>> 4( Intel i5) for data solving. Does anyone know how to
>>>>>>> config CPU so that all processors can be used.
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Chang
>>>>>>>
>>>>
>>>>>
>>>>
>
>>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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