Hi all,
KMC packaging is done.
http://anonscm.debian.org/cgit/debian-med/kmc.git/
Steffen, would you be able to sponsor this package?
Regards,
Jorge
On Mon, Nov 17, 2014 at 8:50 AM, Jorge Sebastião Soares <
j.s.soa...@gmail.com> wrote:
> Hi Marek,
>
> Sorry for the time it took for me to get back to you.
> I am at the point that I have the kmc package ready to be submitted.
> Just doing final tidy ups and automating man page creation for the two
> binaries (kmc and kmc_dump).
> To do this I use help2man which has been proving great for turning any
> kind of usage into man pages.
> I should be done with this by lunch time today.
>
> At the moment, for the creaiton of the kmc debian package I'm using my
> github repository.
> I hope that's ok for you for the moment.
> Once you guys are done with writing the new version of kmc we can point
> the package to look at your own VCS repository.
> Let me know if this ok for now.
>
> On Wed, Nov 12, 2014 at 6:14 PM, Marek Kokot wrote:
>
>> Hello Jorge,
>>
>> Hope all is well.
>>
>> Its fine, thanks. How are you? ;-)
>>
>>
> Great!
> I'm very well as well. :)
>
>
>> Thank you for your tests. I have made a couple of tests on my own and
>> the results was pretty similar to your. As I said it was only couple of
>> tests but on reative big data (human genome about 100 GB gzipped).
>>
>
> Cool!
>
>
>>
>> My question is: Have you used HDD or SSD? I have used HDD, for SSD it
>> is possible that differences in time may be bigger. I will try to test it
>> for SSD.
>>
>
> I was running it on HDD.
> Did you run it on SSD already? Did you get any significant improvement?
>
>
>>
>> I spoke with Sebastian today and we agree that it is a good option to
>> make compilation without asmlib possible. I will deal with this and I let
>> you know when it is ready.
>>
>
> Awesome!
> I'm so glad to hear this.
> This will also mean that KMC will be able to be built for other chips
> other than the intel ones.
> This feature will be available only with the new verison of KMC?
>
>
>>
>> KMC in current version has also "boost" dependency, but we think to go
>> native, because g++ supports c++11 threads. Other functionalities from
>> "boost" that we use are easy to replace with c++11. It should make
>> compilation time shorter for the ones who hasn't "boost" installed.
>>
>
> I see. It does take a while ot compile, but dependency on Boost is
> definitely not an issue from where I'm sitting.
> The package builds properly with the Debian boost, zlib and libbz2
> dependencies.
> I do appreciate that it does take a while to compile.
>
>
>>
>> In one of earlier e-mails you asked about Agner (asmlib author):
>>
>> Do you think it would make sense for me to approach him through the
>> Debian Med team?
>>
>> We would prefer to deal with it on our own.
>>
>> No problem at all.
>
>
>
>> If there is something I ommited and I didn't answer to any of your
>> questions please let me know.
>>
>
> I think you answered everything. I do appologise for stressing you guys
> out with these requests, especially at a time when you're concentrating on
> writing a new release.
>
> Kind regards,
>
> Jorge Soares
>
>
> --
> *Od:* Jorge Sebastião Soares [j.s.soa...@gmail.com]
> *Wysłano:* 11 listopada 2014 18:00
> *Do:* Marek Kokot; Sebastian Deorowicz
> *DW:* Debian Med Project List
> *Temat:* [KMC + asmlib] KMC Debian package progress
>
> Hi guys,
>
> I had to send this again as I used my Sanger email, but that is not
> subscribed to the Debian Med Mailing list.
>
> So here it goes again (if you can ignore the previous one and respond to
> this one).
>
> Hope all is well.
> Have you given any thought to my proposal of a compile time option that
> won't use asmlib?
>
> I have included the Debian Med team on this email as they are aware of the
> packaging of KMC and the whole issue with asmlib.
>
> I have been doing some benchmarking on KMC for the past couple of days.
> I have compiled KMC in three ways:
>
> kmc_original - kmc code compiled against the version of asmlib distributed
> with KMC- alibelf64.a
> kmc_native - kmc code compiled against the native OS libraries
> kmc_js21 - kmc code compiled against the new version of asmlib, compiled
> on my machine with my Unix makefile - libaelf64.a
>
> I have also used the executables provided in your website in the benchmark.
>
> kmc_exe
>
> The machine I used for this is a Debian Virtual Machine running on Vagrant.
>
> Here are the architecture details:
>
> vagrant@debian:~$ cat /proc/cpuinfo
> processor: 0
> vendor_id: GenuineIntel
> cpu family: 6
> model: 23
> model name: Intel(R) Core(TM)2 Duo CPU P8600 @ 2.40GHz
> stepping: 10
> microcode: 0x60b
> cpu MHz: 1426.514
> cache size: 6144 KB
> physical id: 0
> siblings: 1
> core id: 0
> cpu cores: 1
> apicid: 0
> initial apicid: 0
> fpu: yes
> fpu_exception: yes
> cpuid level: 5
> wp
