RNA World - Here we finally go...

[Michael H.W. Weber]

After massive problems, I finally managed to find my way through the registration process on your board. It would actually be nice to have a central button on the front page to switch to english, otherwise it is quite difficult if not impossible for people not capable of reading Czech to communicate with you guys. Fact is, I do not understand a single Czech word although I spent a week in Praha (see, at least ONE Czech word is out now) in December 2006. If people wouldn't understand english very well over there, I couldn't even have ordered a beer at that time - just imagine that one!

Well, to keep it short for now, I think you know what the RNA World project is basically about. If not, just go ahead and ask me - I will drop by here from time to time to check. And yes, we are at a very early stage of project development although we are in DC for 10 years now (initially [and still] as crunchers). Consequently, not everything runs as smoothly as we wish, but this project has to tackle problems that are quite different from those that other projects have. One of these is: We cannot (yet) predict RAM requirements. But I think we already have a solution for the issues with our latest work unit batch which is hopefuly our last "test in the wild" where we really released some demanding stuff.

Let me say thank you to those who reported problems in our forum. Only such feedback allows us to identify and solve problems we had not seen with our local machine testings.

Michael.

P.S.: My personal favourite city in Europe is indeed Praha.
P.P.S.: Wir können auch Deutsch sprechen.

[vkliber]

Welcome to our forum .

[vkliber]

Sorry on difficulties in registering for the forum, we primarily focus on the Czech-speaking community. However, we are happy that you did .

[nenym]

Hi Michael, nice to see you here.

[KPX]

P.P.S.: Wir können auch Deutsch sprechen.

Welcome to our forum, Michael... but please, let's stay with English...

[Michael H.W. Weber]

Thank you for welcoming me here so nicely.

Michael.

[Michael H.W. Weber]

I think we have found a way to solve the huge hardware demands of the very large CMS WUs such that even the smaller machines like those running Windows x86 will be able to participate again in the near future. It will however cost us a bit of programming work, so please have a little patience.

Michael.

P.S.: I am currently staying in India to coordinate a number of things with our cooperation partners over here. So, it is sometimes a bit difficult with Internet access and hence I will be less responsive until mid of April...

[vkliber]

That would be bad choice of applications work?
I had set the application cmsearch to Yes and I updated the project in BOINC Manager

19.3.10 17:51:54 RNA World Message from server: No work sent
19.3.10 17:51:54 RNA World Message from server: cmsearch needs 3814.70 MB RAM but only 3160.87 MB is available for use.

OK, I have little memory, it does not matter .

And now I set the application cmsearch to Not and updated the project in BOINC Manager

19.3.10 19:26:06 RNA World Message from server: No work can be sent for the applications you have selected
19.3.10 19:26:06 RNA World Message from server: No work is available for upperCASE
19.3.10 19:26:06 RNA World Message from server: You have selected to receive work from other applications if no work is available for the applications you selected
19.3.10 19:26:06 RNA World Message from server: Sending work from other applications

And I download WUs of application cmsearch .

[Michael H.W. Weber]

Well, then it seems you identified another bug in the BOINC software. We will check it. Thanks for the information.

Michael.

[MIZ]

Nenym (and others): How to get any "calibrate" WUs? I finished tens of WUs, but all the "cmsearch" only.
My account settings:

Run only the selected applications
upperCASE: no
cmsearch: yes
cmcalibrate: yes

2 machines running this project are 4-core CPU (1 AMD + 1 Intel), 4 GB RAM, Vista 64b.
Sure, it isn't a problem, it's my interest only... So I don't spamming the project forum with this (but with other themes yes ) and asking experienced project users here.

[Michael H.W. Weber]

Hi guys, we have a novel batch of user-friendly WUs ready for processing that deals with tuberculosis while we continue to solve the problem with the huge RAM demands of some of the WUs from the latest batch. For details please see our NEWS section plus the "scientific objectives" page of the RNA World project which I have updated and finalized a few days ago. We also improved the WU delivery settings and implemented a failure counter that prevents a WU from being sent out again if it has not passed validation for a certain number of times.

Michael.

[Michael H.W. Weber]

As described in the projects NEWS section in more detail, we had to transiently disable the WU generator.

Michael.

[Michael H.W. Weber]

The WU generator is working again, the small WUs will now be processed on the server, except for very, very few which we will deliver to some remote machines. Please also note that the server response delay has been drastically reduced such that connection issues should be resolved by now as well. We have plenty of WUs, will not run out of work and hope for your further support which is very much appreciated.

Michael.

P.S.: Our new concept to resolve the massive RAM requirements of our "CMSEARCH Monster WUs" has resulted in a program which is currently in testing phase. So, even here I expect good progress in the upcoming weeks...

[Michael H.W. Weber]

Not a single error-report in two weeks it now seems that our project is running reliable and smoothly. Given the vast amounts of WUs in the server queue, we are actually in need of much more support. So, if you could spare some cycles it would be highly appreciated.

Michael.

[MIZ]

I started it again. All my WUs ended with error "output file absent":

13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanosarcina-mazei-Go1_AE008384.cir.EMBL_RF00383_IS1222_FSE_1273713427_27270_1_0 for task cms_GA[a-Lin64s]_Methanosarcina-mazei-Go1_AE008384.cir.EMBL_RF00383_IS1222_FSE_1273713427_27270_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanococcus-aeolicus-Nankai-3_CP000743.cir.EMBL_RF00373_RNaseP_arch_1273713427_26518_1_0 for task cms_GA[a-Lin64s]_Methanococcus-aeolicus-Nankai-3_CP000743.cir.EMBL_RF00373_RNaseP_arch_1273713427_26518_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanoculleus-marisnigri-JR1_CP000562.cir.EMBL_RF00421_SNORA32_1273713427_30003_1_0 for task cms_GA[a-Lin64s]_Methanoculleus-marisnigri-JR1_CP000562.cir.EMBL_RF00421_SNORA32_1273713427_30003_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Haloquadratum-walsbyi_AM180088.cir.EMBL_RF00421_SNORA32_1273713427_29983_1_0 for task cms_GA[a-Lin64s]_Haloquadratum-walsbyi_AM180088.cir.EMBL_RF00421_SNORA32_1273713427_29983_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Haloarcula-marismortui-ATCC-43049_AY596297.cir.EMBL_RF00420_SNORA61_1273713427_29904_1_0 for task cms_GA[a-Lin64s]_Haloarcula-marismortui-ATCC-43049_AY596297.cir.EMBL_RF00420_SNORA61_1273713427_29904_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-abyssi-GE5_AL096836.cir.EMBL_RF00438_SNORA33_1273713427_31279_1_0 for task cms_GA[a-Lin64s]_Pyrococcus-abyssi-GE5_AL096836.cir.EMBL_RF00438_SNORA33_1273713427_31279_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Methanocaldococcus-jannaschii-DSM-2661_L77117.cir.EMBL_RF00438_SNORA33_1273713427_31250_1_0 for task cms_GA[a-Lin64s]_Methanocaldococcus-jannaschii-DSM-2661_L77117.cir.EMBL_RF00438_SNORA33_1273713427_31250_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Methanobrevibacter-smithii-ATCC-35061_CP000678.cir.EMBL_RF00438_SNORA33_1273713427_31248_1_0 for task cms_GA[a-Lin64s]_Methanobrevibacter-smithii-ATCC-35061_CP000678.cir.EMBL_RF00438_SNORA33_1273713427_31248_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Metallosphaera-sedula-DSM-5348_CP000682.cir.EMBL_RF00438_SNORA33_1273713427_31247_1_0 for task cms_GA[a-Lin64s]_Metallosphaera-sedula-DSM-5348_CP000682.cir.EMBL_RF00438_SNORA33_1273713427_31247_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00442_ykkC-yxkD_1273713427_31576_1_0 for task cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00442_ykkC-yxkD_1273713427_31576_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00441_snoZ242_1273713427_31502_0_0 for task cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00441_snoZ242_1273713427_31502_0 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrobaculum-islandicum-DSM-4184_CP000504.cir.EMBL_RF00441_snoZ242_1273713427_31500_1_0 for task cms_GA[a-Lin64s]_Pyrobaculum-islandicum-DSM-4184_CP000504.cir.EMBL_RF00441_snoZ242_1273713427_31500_1 absent

Win 7 64b, BM 6.10.50 64b

[Michael H.W. Weber]

Well, that would be a new one. Your RNA World username, please?

Michael.

P.S.: I assume BOINC has write right on your HD and you have not altered anything in your RNA World work directory such as deleting files or re-installing BOINC, of course...

[vkliber]

MIZ from team Space Family.

[yoyo]

I started it again. All my WUs ended with error "output file absent":

13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanosarcina-mazei-Go1_AE008384.cir.EMBL_RF00383_IS1222_FSE_1273713427_27270_1_0 for task cms_GA[a-Lin64s]_Methanosarcina-mazei-Go1_AE008384.cir.EMBL_RF00383_IS1222_FSE_1273713427_27270_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanococcus-aeolicus-Nankai-3_CP000743.cir.EMBL_RF00373_RNaseP_arch_1273713427_26518_1_0 for task cms_GA[a-Lin64s]_Methanococcus-aeolicus-Nankai-3_CP000743.cir.EMBL_RF00373_RNaseP_arch_1273713427_26518_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanoculleus-marisnigri-JR1_CP000562.cir.EMBL_RF00421_SNORA32_1273713427_30003_1_0 for task cms_GA[a-Lin64s]_Methanoculleus-marisnigri-JR1_CP000562.cir.EMBL_RF00421_SNORA32_1273713427_30003_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Haloquadratum-walsbyi_AM180088.cir.EMBL_RF00421_SNORA32_1273713427_29983_1_0 for task cms_GA[a-Lin64s]_Haloquadratum-walsbyi_AM180088.cir.EMBL_RF00421_SNORA32_1273713427_29983_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Haloarcula-marismortui-ATCC-43049_AY596297.cir.EMBL_RF00420_SNORA61_1273713427_29904_1_0 for task cms_GA[a-Lin64s]_Haloarcula-marismortui-ATCC-43049_AY596297.cir.EMBL_RF00420_SNORA61_1273713427_29904_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-abyssi-GE5_AL096836.cir.EMBL_RF00438_SNORA33_1273713427_31279_1_0 for task cms_GA[a-Lin64s]_Pyrococcus-abyssi-GE5_AL096836.cir.EMBL_RF00438_SNORA33_1273713427_31279_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Methanocaldococcus-jannaschii-DSM-2661_L77117.cir.EMBL_RF00438_SNORA33_1273713427_31250_1_0 for task cms_GA[a-Lin64s]_Methanocaldococcus-jannaschii-DSM-2661_L77117.cir.EMBL_RF00438_SNORA33_1273713427_31250_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Methanobrevibacter-smithii-ATCC-35061_CP000678.cir.EMBL_RF00438_SNORA33_1273713427_31248_1_0 for task cms_GA[a-Lin64s]_Methanobrevibacter-smithii-ATCC-35061_CP000678.cir.EMBL_RF00438_SNORA33_1273713427_31248_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Metallosphaera-sedula-DSM-5348_CP000682.cir.EMBL_RF00438_SNORA33_1273713427_31247_1_0 for task cms_GA[a-Lin64s]_Metallosphaera-sedula-DSM-5348_CP000682.cir.EMBL_RF00438_SNORA33_1273713427_31247_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00442_ykkC-yxkD_1273713427_31576_1_0 for task cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00442_ykkC-yxkD_1273713427_31576_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00441_snoZ242_1273713427_31502_0_0 for task cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00441_snoZ242_1273713427_31502_0 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrobaculum-islandicum-DSM-4184_CP000504.cir.EMBL_RF00441_snoZ242_1273713427_31500_1_0 for task cms_GA[a-Lin64s]_Pyrobaculum-islandicum-DSM-4184_CP000504.cir.EMBL_RF00441_snoZ242_1273713427_31500_1 absent

Win 7 64b, BM 6.10.50 64b

All your workunits failed with:

wrapper: running unzip (-o graphics.zip)
can't run app: -148

Running unzip failed. The workunits which I checked has finished on some other hosts without any problems. I don't know why unzip on your PC failed. Maybe your virus scanner has removed it.

yoyo

[Michael H.W. Weber]

I started it again. All my WUs ended with error "output file absent":

13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanosarcina-mazei-Go1_AE008384.cir.EMBL_RF00383_IS1222_FSE_1273713427_27270_1_0 for task cms_GA[a-Lin64s]_Methanosarcina-mazei-Go1_AE008384.cir.EMBL_RF00383_IS1222_FSE_1273713427_27270_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanococcus-aeolicus-Nankai-3_CP000743.cir.EMBL_RF00373_RNaseP_arch_1273713427_26518_1_0 for task cms_GA[a-Lin64s]_Methanococcus-aeolicus-Nankai-3_CP000743.cir.EMBL_RF00373_RNaseP_arch_1273713427_26518_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Methanoculleus-marisnigri-JR1_CP000562.cir.EMBL_RF00421_SNORA32_1273713427_30003_1_0 for task cms_GA[a-Lin64s]_Methanoculleus-marisnigri-JR1_CP000562.cir.EMBL_RF00421_SNORA32_1273713427_30003_1 absent
13.5.2010 22:28:04 RNA World Output file cms_GA[a-Lin64s]_Haloquadratum-walsbyi_AM180088.cir.EMBL_RF00421_SNORA32_1273713427_29983_1_0 for task cms_GA[a-Lin64s]_Haloquadratum-walsbyi_AM180088.cir.EMBL_RF00421_SNORA32_1273713427_29983_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Haloarcula-marismortui-ATCC-43049_AY596297.cir.EMBL_RF00420_SNORA61_1273713427_29904_1_0 for task cms_GA[a-Lin64s]_Haloarcula-marismortui-ATCC-43049_AY596297.cir.EMBL_RF00420_SNORA61_1273713427_29904_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-abyssi-GE5_AL096836.cir.EMBL_RF00438_SNORA33_1273713427_31279_1_0 for task cms_GA[a-Lin64s]_Pyrococcus-abyssi-GE5_AL096836.cir.EMBL_RF00438_SNORA33_1273713427_31279_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Methanocaldococcus-jannaschii-DSM-2661_L77117.cir.EMBL_RF00438_SNORA33_1273713427_31250_1_0 for task cms_GA[a-Lin64s]_Methanocaldococcus-jannaschii-DSM-2661_L77117.cir.EMBL_RF00438_SNORA33_1273713427_31250_1 absent
13.5.2010 22:30:28 RNA World Output file cms_GA[a-Lin64s]_Methanobrevibacter-smithii-ATCC-35061_CP000678.cir.EMBL_RF00438_SNORA33_1273713427_31248_1_0 for task cms_GA[a-Lin64s]_Methanobrevibacter-smithii-ATCC-35061_CP000678.cir.EMBL_RF00438_SNORA33_1273713427_31248_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Metallosphaera-sedula-DSM-5348_CP000682.cir.EMBL_RF00438_SNORA33_1273713427_31247_1_0 for task cms_GA[a-Lin64s]_Metallosphaera-sedula-DSM-5348_CP000682.cir.EMBL_RF00438_SNORA33_1273713427_31247_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00442_ykkC-yxkD_1273713427_31576_1_0 for task cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00442_ykkC-yxkD_1273713427_31576_1 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00441_snoZ242_1273713427_31502_0_0 for task cms_GA[a-Lin64s]_Pyrococcus-furiosus-DSM-3638_AE009950.cir.EMBL_RF00441_snoZ242_1273713427_31502_0 absent
13.5.2010 22:32:55 RNA World Output file cms_GA[a-Lin64s]_Pyrobaculum-islandicum-DSM-4184_CP000504.cir.EMBL_RF00441_snoZ242_1273713427_31500_1_0 for task cms_GA[a-Lin64s]_Pyrobaculum-islandicum-DSM-4184_CP000504.cir.EMBL_RF00441_snoZ242_1273713427_31500_1 absent

Win 7 64b, BM 6.10.50 64b

Well, it seems that this error indeed is located at your end: For unknown reason, your unzip does not work properly or a virus scanner has removed something:

Kód: Vybrat vše

wrapper: running unzip (-o graphics.zip)
can't run app: -148

Michael.

[MIZ]

OK, I'll check my security software settings...
Thanks