| Posted | Nick | Remark | |
|---|---|---|---|
| #openstack-cyborg - 2017-11-15 | |||
| 08:38:04 | masber | I think intel got GATK4 running on FPGAs | |
| 08:38:05 | zhipengh[m] | With a real use case :) | |
| 08:38:27 | masber | yes my use case is quite real because we are planing to deploy this pipeline in production | |
| 08:38:38 | masber | we are actually running GATK3 in production | |
| 08:38:41 | zhipengh[m] | BTW we will have video conference about 6:20 hour later | |
| 08:38:51 | zhipengh[m] | Would it be possible for you to join ? | |
| 08:39:03 | masber | in 6.20 hours | |
| 08:39:06 | masber | let me check | |
| 08:39:11 | zhipengh[m] | Haha right | |
| 08:39:21 | masber | 2:00 am my time | |
| 08:39:28 | masber | yes I can join | |
| 08:39:56 | zhipengh[m] | Wow that is pretty late | |
| 08:40:20 | zhipengh[m] | Anyways I will send out the details later on openstack-dev mailing list | |
| 08:40:32 | masber | yep, well as I said Im not a quite competent openstack user so most of the time I have to stay till late so I can get help from the community | |
| 08:40:47 | masber | many nights working until 4am | |
| 08:41:02 | masber | but it is ok, I am happy to try and see if I can help you | |
| 08:41:02 | zhipengh[m] | Man that is hardcore | |
| 08:41:18 | masber | my boss gives me free days | |
| 08:41:20 | masber | it is ok | |
| 08:41:45 | zhipengh[m] | :) | |
| 08:42:11 | masber | plus I'm a pragmatic person which means I learn by experience so for me it is quite good to get in contact with people in get things done | |
| 08:42:15 | masber | anyway | |
| 08:42:51 | masber | yeah I will join the call so if there any doubt I can talk with the intel guy tomorrow | |
| 08:43:03 | masber | he is giving me the cards and then we will have a meeting | |
| 08:43:21 | masber | so maybe I can ask questions in your behalf | |
| 08:46:47 | masber | so how do you do the video conference? | |
| 08:47:10 | masber | skype? | |
| 08:47:17 | masber | google hangouts? | |
| 08:48:59 | zhipengh[m] | ZOOM | |
| 08:50:21 | zhipengh[m] | Very good quality | |
| 08:50:28 | masber | ok | |
| 08:53:27 | masber | ok I will see you later, Im going home now | |
| 08:59:16 | zhipengh[m] | Take care man ! | |
| 14:56:08 | masuberu | hi | |
| 14:56:32 | masuberu | is the meeting happening? | |
| 14:57:55 | zhipeng | hi will start momentarily | |
| 14:58:28 | masuberu | ok | |
| 14:58:38 | masuberu | I don't know how to access tho | |
| 14:59:09 | masuberu | and also I can't talk as it is 2am and everybody is sleeping at home but I can chat and listen | |
| 15:00:16 | masuberu | just ping me when people is ready | |
| 15:00:19 | zhipeng | okey no problem, let me send the zoom link here | |
| 15:00:29 | zhipeng | #startmeeting openstack-cyborg | |
| 15:00:29 | openstack | Meeting started Wed Nov 15 15:00:29 2017 UTC and is due to finish in 60 minutes. The chair is zhipeng. Information about MeetBot at http://wiki.debian.org/MeetBot. | |
| 15:00:30 | openstack | Useful Commands: #action #agreed #help #info #idea #link #topic #startvote. | |
| 15:00:33 | openstack | The meeting name has been set to 'openstack_cyborg' | |
| 15:01:25 | zhipeng | #link https://zoom.us/j/973513277 | |
| 15:06:03 | zhipeng | just did a little bit chatting with crushil, that we will keep irc meeting today, and move the zoom meeting to a later time slot for dev specific issue | |
| 15:06:14 | zhipeng | will keep everybody posted | |
| 15:07:29 | masuberu | so no zoom, just irc for now? | |
| 15:08:29 | zhipeng | masuberu yep :) | |
| 15:08:36 | zhipeng | crushil you there ? | |
| 15:09:03 | masuberu | ok | |
| 15:09:05 | shaohe_feng_ | zhipeng: what's the zoom conference ID? | |
| 15:09:26 | zhipeng | shaohe_feng_ will do zoom tomorrow morning | |
| 15:09:54 | shaohe_feng_ | zhipeng: got it. | |
| 15:10:01 | zhipeng | could everyone log their names ? | |
| 15:10:04 | zhipeng | #info Howard | |
| 15:10:23 | zhuli | Can’t get my pc connected, have to use cellphone | |
| 15:10:32 | mpaolino | #info Michele | |
| 15:10:41 | Guest69871 | #info Li | |
| 15:10:41 | zhipeng | zhuli we will just irc tonight | |
| 15:10:42 | zhuli | #info zhuli | |
| 15:10:51 | zhuli | Got it | |
| 15:11:01 | Guest69871 | Do we have another meeting tomorrow? | |
| 15:11:20 | crushil | I'm here | |
| 15:11:35 | zhipeng | okey seems like full house almost :) | |
| 15:11:36 | crushil | #info Rushil | |
| 15:11:58 | zhipeng | #topic GATK4 FPGA requirement discussion | |
| 15:12:23 | zhipeng | the first order of business today is that we have masuberu | |
| 15:12:49 | masuberu | o/ | |
| 15:12:54 | zhipeng | system engineer from one of the largest genome testing reserach testing centers in the world | |
| 15:13:05 | zhuli | Welcome masuberu | |
| 15:13:19 | masuberu | thank you all for having me here | |
| 15:13:33 | zhipeng | to talk with us about their upcoming trail with Intel FPGA card to run GTAK4 application for genome analysis | |
| 15:13:42 | zhipeng | the floor is yours masuberu :) | |
| 15:13:50 | masuberu | than you | |
| 15:14:05 | masuberu | I work for a medical research intitute | |
| 15:14:16 | masuberu | and as sequence and analyse genomes | |
| 15:14:22 | shaohe_feng__ | #info shaohe | |
| 15:14:29 | masuberu | right now we are in a project with intel | |
| 15:15:04 | masuberu | they are helping us to build an environment to run GATK4 which a set of tools of best practice genome analysis | |
| 15:15:25 | masuberu | tomorrow a guy from intel is coming to my office to give me FPGA cards | |
| 15:15:50 | masuberu | because GATK4 can either work on HPC cluster, Spark cluster and GDC | |
| 15:16:16 | masuberu | so my idea is to test GATK4 on FPGAs through openstack and compare performance with apache spark | |
| 15:16:36 | masuberu | obviously FPGA should be much faster but we want to see how much faster | |
| 15:17:25 | masuberu | and I was looking for documentation about how to integrate FPGAs on openstack and I found your project | |
| 15:17:52 | zhipeng | shaohe_feng_ is from Intel :) | |
| 15:17:53 | masuberu | so wanted to say hi and see if this would be a possibility of collaboration | |
| 15:18:02 | masuberu | ok | |
| 15:18:10 | masuberu | well intel is quite big | |
| 15:18:12 | masuberu | I guess | |
| 15:18:16 | shaohe_feng__ | masuberu: hi | |
| 15:18:22 | zhipeng | haha yes | |
| 15:18:33 | Guest69871 | Hi Masuberu, This is Li from Huawei, our team has a lot of experience using FPGAs in Openstack | |
| 15:18:36 | masuberu | the person coming tomorrow is from either China or Singapore I think | |
| 15:18:58 | zhipeng | masuberu could you describe a possible setup ? | |
| 15:19:20 | zhipeng | For example if you are gonna have a VM connected to the FPGA | |
| 15:19:38 | zhipeng | or just feeding data directly to GTAK4 on that FPGA ? | |
| 15:20:04 | masuberu | what ever is easier, I was thinking of giving a go and see if could be possible to integrate FPGAs with nova and see if the vms could see it | |
| 15:20:13 | shaohe_feng__ | masuberu: I'm also working on FPGA. And some of us has started to support FPGA on k8s | |