Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
Right! I did think to look for a 'share this cluster' command, I just failed to find it. It all makes sense now, thanks. On Thu, Dec 1, 2011 at 7:34 PM, Enis Afgan wrote: > Hi Clare, > The share string is generated when you share a cluster. The string is > accessible on the shared cluster, when you click the green 'Share a cluster' > icon next to the cluster name and then the top link "Shared instances". You > will get a list of the point in time shares of the cluster you have created. > The share string will look something like > this cm-cd53Bfg6f1223f966914df347687f6uf32/shared/2011-10-19--03-14 > You simply paste that string into new cluster box you mentioned. > Enis > > On Thu, Dec 1, 2011 at 6:31 AM, Clare Sloggett wrote: >> >> Hi Enis, Jeremy, and all, >> >> Thanks so much for all your help. I have another question which I >> suspect is just me missing something obvious. >> >> I'm guessing that when you cloned the cluster for your workshop, you >> used CloudMan's 'share-an-instance' functionality? >> When I launch a new cluster which I want to be a copy of an existing >> cluster, and select the share-an-instance option, it asks for the >> "cluster share-string". How can I find this string for my existing >> cluster? >> >> Or have I got completely the wrong idea - did you actually clone the >> instance using AWS functionality? >> >> Thanks, >> Clare >> >> On Mon, Nov 21, 2011 at 5:37 PM, Enis Afgan wrote: >> > Hi Clare, >> > I don't recall what instance type we used earlier, but I think an Extra >> > Large Instance is going to be fine. Do note that the master node is also >> > being used to run jobs. However, if it's loaded by just the web server, >> > SGE >> > will typically just not schedule jobs to it. >> > >> > As far as the core/thread/slot concerns goes, SGE sees each core as a >> > slot. >> > Each job in Galaxy simply requires 1 slot, even if it uses multiple >> > threads >> > (i.e., cores). What this means is that nodes will probably get >> > overloaded if >> > only the same type of job is being run (BWA), but if analyses are being >> > run >> > that use multiple tools, jobs will get spread over the cluster to >> > balance >> > the overal load a bit better than by simply looking at the number of >> > slots. >> > >> > Enis >> > >> > On Mon, Nov 21, 2011 at 4:34 AM, Clare Sloggett >> > wrote: >> >> >> >> Hi Jeremy, >> >> >> >> Also if you do remember what kind of Amazon node you used, >> >> particularly for the cluster's master node (e.g. an 'xlarge' 4-core >> >> 15GB or perhaps one of the 'high-memory' nodes?), that would be a >> >> reassuring sanity chech for me! >> >> >> >> Cheers, >> >> Clare >> >> >> >> On Mon, Nov 21, 2011 at 10:37 AM, Clare Sloggett >> >> wrote: >> >> > Hi Jeremy, Enis, >> >> > >> >> > That makes sense. I know I can configure how many threads BWA uses in >> >> > its wrapper, with bwa -t. But, is there somewhere that I need to tell >> >> > Galaxy the corresponding information, ie that this command-line task >> >> > will make use of up to 4 cores? >> >> > >> >> > Or, does this imply that there is always exactly one job per node? So >> >> > if I have (for instance) a cluster made of 4-core nodes, and a >> >> > single-threaded task (e.g. samtools), are the other 3 cores just >> >> > going >> >> > to waste or will the scheduler allocate multiple single-threaded jobs >> >> > to one node? >> >> > >> >> > I've cc'd galaxy-dev instead of galaxy-user as I think the >> >> > conversation has gone that way! >> >> > >> >> > Thanks again, >> >> > Clare >> >> > >> >> > >> >> > On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks >> >> > >> >> > wrote: >> >> >> >> >> >>> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks >> >> >>> wrote: >> >> >>> >> >> Scalability issues are more likely to arise on the back end than >> >> the >> >> front end, so you'll want to ensure that you have enough compute >> >> nodes. BWA >> >> uses four nodes by default--Enis, does the cloud config change >> >> this >> >> parameter?--so you'll want 4x50 or 200 total nodes if you want >> >> everyone to >> >> be able to run a BWA job simultaneously. >> >> >> >> >>> >> >> >>> Actually, one other question - this paragraph makes me realise that >> >> >>> I >> >> >>> don't really understand how Galaxy is distributing jobs. I had >> >> >>> thought >> >> >>> that each job would only use one node, and in some cases take >> >> >>> advantage of multiple cores within that node. I'm taking a "node" >> >> >>> to >> >> >>> be a set of cores with their own shared memory, so in this case a >> >> >>> VM >> >> >>> instance, is this right? If some types of jobs can be distributed >> >> >>> over >> >> >>> multiple nodes, can I configure, in Galaxy, how many nodes they >> >> >>> should >> >> >>> use? >> >> >> >> >> >> You're right -- my word choices were poor. Replace 'node' with >> >> >> 'core' >> >> >> in my paragraph to get an accurate suggestion for resources. >> >> >> >> >> >> Gala
Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
Hi Clare, The share string is generated when you share a cluster. The string is accessible on the shared cluster, when you click the green 'Share a cluster' icon next to the cluster name and then the top link "Shared instances". You will get a list of the point in time shares of the cluster you have created. The share string will look something like this cm-cd53Bfg6f1223f966914df347687f6uf32/shared/2011-10-19--03-14 You simply paste that string into new cluster box you mentioned. Enis On Thu, Dec 1, 2011 at 6:31 AM, Clare Sloggett wrote: > Hi Enis, Jeremy, and all, > > Thanks so much for all your help. I have another question which I > suspect is just me missing something obvious. > > I'm guessing that when you cloned the cluster for your workshop, you > used CloudMan's 'share-an-instance' functionality? > When I launch a new cluster which I want to be a copy of an existing > cluster, and select the share-an-instance option, it asks for the > "cluster share-string". How can I find this string for my existing > cluster? > > Or have I got completely the wrong idea - did you actually clone the > instance using AWS functionality? > > Thanks, > Clare > > On Mon, Nov 21, 2011 at 5:37 PM, Enis Afgan wrote: > > Hi Clare, > > I don't recall what instance type we used earlier, but I think an Extra > > Large Instance is going to be fine. Do note that the master node is also > > being used to run jobs. However, if it's loaded by just the web server, > SGE > > will typically just not schedule jobs to it. > > > > As far as the core/thread/slot concerns goes, SGE sees each core as a > slot. > > Each job in Galaxy simply requires 1 slot, even if it uses multiple > threads > > (i.e., cores). What this means is that nodes will probably get > overloaded if > > only the same type of job is being run (BWA), but if analyses are being > run > > that use multiple tools, jobs will get spread over the cluster to balance > > the overal load a bit better than by simply looking at the number of > slots. > > > > Enis > > > > On Mon, Nov 21, 2011 at 4:34 AM, Clare Sloggett > wrote: > >> > >> Hi Jeremy, > >> > >> Also if you do remember what kind of Amazon node you used, > >> particularly for the cluster's master node (e.g. an 'xlarge' 4-core > >> 15GB or perhaps one of the 'high-memory' nodes?), that would be a > >> reassuring sanity chech for me! > >> > >> Cheers, > >> Clare > >> > >> On Mon, Nov 21, 2011 at 10:37 AM, Clare Sloggett > >> wrote: > >> > Hi Jeremy, Enis, > >> > > >> > That makes sense. I know I can configure how many threads BWA uses in > >> > its wrapper, with bwa -t. But, is there somewhere that I need to tell > >> > Galaxy the corresponding information, ie that this command-line task > >> > will make use of up to 4 cores? > >> > > >> > Or, does this imply that there is always exactly one job per node? So > >> > if I have (for instance) a cluster made of 4-core nodes, and a > >> > single-threaded task (e.g. samtools), are the other 3 cores just going > >> > to waste or will the scheduler allocate multiple single-threaded jobs > >> > to one node? > >> > > >> > I've cc'd galaxy-dev instead of galaxy-user as I think the > >> > conversation has gone that way! > >> > > >> > Thanks again, > >> > Clare > >> > > >> > > >> > On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks < > jeremy.goe...@emory.edu> > >> > wrote: > >> >> > >> >>> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks > >> >>> wrote: > >> >>> > >> Scalability issues are more likely to arise on the back end than > the > >> front end, so you'll want to ensure that you have enough compute > nodes. BWA > >> uses four nodes by default--Enis, does the cloud config change this > >> parameter?--so you'll want 4x50 or 200 total nodes if you want > everyone to > >> be able to run a BWA job simultaneously. > >> > >> >>> > >> >>> Actually, one other question - this paragraph makes me realise that > I > >> >>> don't really understand how Galaxy is distributing jobs. I had > thought > >> >>> that each job would only use one node, and in some cases take > >> >>> advantage of multiple cores within that node. I'm taking a "node" to > >> >>> be a set of cores with their own shared memory, so in this case a VM > >> >>> instance, is this right? If some types of jobs can be distributed > over > >> >>> multiple nodes, can I configure, in Galaxy, how many nodes they > should > >> >>> use? > >> >> > >> >> You're right -- my word choices were poor. Replace 'node' with 'core' > >> >> in my paragraph to get an accurate suggestion for resources. > >> >> > >> >> Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to > >> >> different cluster nodes. Jobs that require multiple cores typically > run on a > >> >> single node. Enis can chime in on whether CloudMan supports job > submission > >> >> over multiple nodes; this would require setup of an appropriate > parallel > >> >> environment and a tool that can make use of this environment. > >> >> > >>
Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
Hi Enis, Jeremy, and all, Thanks so much for all your help. I have another question which I suspect is just me missing something obvious. I'm guessing that when you cloned the cluster for your workshop, you used CloudMan's 'share-an-instance' functionality? When I launch a new cluster which I want to be a copy of an existing cluster, and select the share-an-instance option, it asks for the "cluster share-string". How can I find this string for my existing cluster? Or have I got completely the wrong idea - did you actually clone the instance using AWS functionality? Thanks, Clare On Mon, Nov 21, 2011 at 5:37 PM, Enis Afgan wrote: > Hi Clare, > I don't recall what instance type we used earlier, but I think an Extra > Large Instance is going to be fine. Do note that the master node is also > being used to run jobs. However, if it's loaded by just the web server, SGE > will typically just not schedule jobs to it. > > As far as the core/thread/slot concerns goes, SGE sees each core as a slot. > Each job in Galaxy simply requires 1 slot, even if it uses multiple threads > (i.e., cores). What this means is that nodes will probably get overloaded if > only the same type of job is being run (BWA), but if analyses are being run > that use multiple tools, jobs will get spread over the cluster to balance > the overal load a bit better than by simply looking at the number of slots. > > Enis > > On Mon, Nov 21, 2011 at 4:34 AM, Clare Sloggett wrote: >> >> Hi Jeremy, >> >> Also if you do remember what kind of Amazon node you used, >> particularly for the cluster's master node (e.g. an 'xlarge' 4-core >> 15GB or perhaps one of the 'high-memory' nodes?), that would be a >> reassuring sanity chech for me! >> >> Cheers, >> Clare >> >> On Mon, Nov 21, 2011 at 10:37 AM, Clare Sloggett >> wrote: >> > Hi Jeremy, Enis, >> > >> > That makes sense. I know I can configure how many threads BWA uses in >> > its wrapper, with bwa -t. But, is there somewhere that I need to tell >> > Galaxy the corresponding information, ie that this command-line task >> > will make use of up to 4 cores? >> > >> > Or, does this imply that there is always exactly one job per node? So >> > if I have (for instance) a cluster made of 4-core nodes, and a >> > single-threaded task (e.g. samtools), are the other 3 cores just going >> > to waste or will the scheduler allocate multiple single-threaded jobs >> > to one node? >> > >> > I've cc'd galaxy-dev instead of galaxy-user as I think the >> > conversation has gone that way! >> > >> > Thanks again, >> > Clare >> > >> > >> > On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks >> > wrote: >> >> >> >>> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks >> >>> wrote: >> >>> >> Scalability issues are more likely to arise on the back end than the >> front end, so you'll want to ensure that you have enough compute nodes. >> BWA >> uses four nodes by default--Enis, does the cloud config change this >> parameter?--so you'll want 4x50 or 200 total nodes if you want everyone >> to >> be able to run a BWA job simultaneously. >> >> >>> >> >>> Actually, one other question - this paragraph makes me realise that I >> >>> don't really understand how Galaxy is distributing jobs. I had thought >> >>> that each job would only use one node, and in some cases take >> >>> advantage of multiple cores within that node. I'm taking a "node" to >> >>> be a set of cores with their own shared memory, so in this case a VM >> >>> instance, is this right? If some types of jobs can be distributed over >> >>> multiple nodes, can I configure, in Galaxy, how many nodes they should >> >>> use? >> >> >> >> You're right -- my word choices were poor. Replace 'node' with 'core' >> >> in my paragraph to get an accurate suggestion for resources. >> >> >> >> Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to >> >> different cluster nodes. Jobs that require multiple cores typically run >> >> on a >> >> single node. Enis can chime in on whether CloudMan supports job submission >> >> over multiple nodes; this would require setup of an appropriate parallel >> >> environment and a tool that can make use of this environment. >> >> >> >> Good luck, >> >> J. >> >> >> >> >> >> >> >> >> > >> > >> > >> > -- >> > E: s...@unimelb.edu.au >> > P: 03 903 53357 >> > M: 0414 854 759 >> > >> >> >> >> -- >> E: s...@unimelb.edu.au >> P: 03 903 53357 >> M: 0414 854 759 > > -- E: s...@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
Hi Clare, I don't recall what instance type we used earlier, but I think an Extra Large Instance is going to be fine. Do note that the master node is also being used to run jobs. However, if it's loaded by just the web server, SGE will typically just not schedule jobs to it. As far as the core/thread/slot concerns goes, SGE sees each core as a slot. Each job in Galaxy simply requires 1 slot, even if it uses multiple threads (i.e., cores). What this means is that nodes will probably get overloaded if only the same type of job is being run (BWA), but if analyses are being run that use multiple tools, jobs will get spread over the cluster to balance the overal load a bit better than by simply looking at the number of slots. Enis On Mon, Nov 21, 2011 at 4:34 AM, Clare Sloggett wrote: > Hi Jeremy, > > Also if you do remember what kind of Amazon node you used, > particularly for the cluster's master node (e.g. an 'xlarge' 4-core > 15GB or perhaps one of the 'high-memory' nodes?), that would be a > reassuring sanity chech for me! > > Cheers, > Clare > > On Mon, Nov 21, 2011 at 10:37 AM, Clare Sloggett > wrote: > > Hi Jeremy, Enis, > > > > That makes sense. I know I can configure how many threads BWA uses in > > its wrapper, with bwa -t. But, is there somewhere that I need to tell > > Galaxy the corresponding information, ie that this command-line task > > will make use of up to 4 cores? > > > > Or, does this imply that there is always exactly one job per node? So > > if I have (for instance) a cluster made of 4-core nodes, and a > > single-threaded task (e.g. samtools), are the other 3 cores just going > > to waste or will the scheduler allocate multiple single-threaded jobs > > to one node? > > > > I've cc'd galaxy-dev instead of galaxy-user as I think the > > conversation has gone that way! > > > > Thanks again, > > Clare > > > > > > On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks > wrote: > >> > >>> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks < > jeremy.goe...@emory.edu> wrote: > >>> > Scalability issues are more likely to arise on the back end than the > front end, so you'll want to ensure that you have enough compute nodes. BWA > uses four nodes by default--Enis, does the cloud config change this > parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to > be able to run a BWA job simultaneously. > > >>> > >>> Actually, one other question - this paragraph makes me realise that I > >>> don't really understand how Galaxy is distributing jobs. I had thought > >>> that each job would only use one node, and in some cases take > >>> advantage of multiple cores within that node. I'm taking a "node" to > >>> be a set of cores with their own shared memory, so in this case a VM > >>> instance, is this right? If some types of jobs can be distributed over > >>> multiple nodes, can I configure, in Galaxy, how many nodes they should > >>> use? > >> > >> You're right -- my word choices were poor. Replace 'node' with 'core' > in my paragraph to get an accurate suggestion for resources. > >> > >> Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to > different cluster nodes. Jobs that require multiple cores typically run on > a single node. Enis can chime in on whether CloudMan supports job > submission over multiple nodes; this would require setup of an appropriate > parallel environment and a tool that can make use of this environment. > >> > >> Good luck, > >> J. > >> > >> > >> > >> > > > > > > > > -- > > E: s...@unimelb.edu.au > > P: 03 903 53357 > > M: 0414 854 759 > > > > > > -- > E: s...@unimelb.edu.au > P: 03 903 53357 > M: 0414 854 759 > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
Hi Jeremy, Also if you do remember what kind of Amazon node you used, particularly for the cluster's master node (e.g. an 'xlarge' 4-core 15GB or perhaps one of the 'high-memory' nodes?), that would be a reassuring sanity chech for me! Cheers, Clare On Mon, Nov 21, 2011 at 10:37 AM, Clare Sloggett wrote: > Hi Jeremy, Enis, > > That makes sense. I know I can configure how many threads BWA uses in > its wrapper, with bwa -t. But, is there somewhere that I need to tell > Galaxy the corresponding information, ie that this command-line task > will make use of up to 4 cores? > > Or, does this imply that there is always exactly one job per node? So > if I have (for instance) a cluster made of 4-core nodes, and a > single-threaded task (e.g. samtools), are the other 3 cores just going > to waste or will the scheduler allocate multiple single-threaded jobs > to one node? > > I've cc'd galaxy-dev instead of galaxy-user as I think the > conversation has gone that way! > > Thanks again, > Clare > > > On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks > wrote: >> >>> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks >>> wrote: >>> Scalability issues are more likely to arise on the back end than the front end, so you'll want to ensure that you have enough compute nodes. BWA uses four nodes by default--Enis, does the cloud config change this parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to be able to run a BWA job simultaneously. >>> >>> Actually, one other question - this paragraph makes me realise that I >>> don't really understand how Galaxy is distributing jobs. I had thought >>> that each job would only use one node, and in some cases take >>> advantage of multiple cores within that node. I'm taking a "node" to >>> be a set of cores with their own shared memory, so in this case a VM >>> instance, is this right? If some types of jobs can be distributed over >>> multiple nodes, can I configure, in Galaxy, how many nodes they should >>> use? >> >> You're right -- my word choices were poor. Replace 'node' with 'core' in my >> paragraph to get an accurate suggestion for resources. >> >> Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to >> different cluster nodes. Jobs that require multiple cores typically run on a >> single node. Enis can chime in on whether CloudMan supports job submission >> over multiple nodes; this would require setup of an appropriate parallel >> environment and a tool that can make use of this environment. >> >> Good luck, >> J. >> >> >> >> > > > > -- > E: s...@unimelb.edu.au > P: 03 903 53357 > M: 0414 854 759 > -- E: s...@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop
Hi Jeremy, Enis, That makes sense. I know I can configure how many threads BWA uses in its wrapper, with bwa -t. But, is there somewhere that I need to tell Galaxy the corresponding information, ie that this command-line task will make use of up to 4 cores? Or, does this imply that there is always exactly one job per node? So if I have (for instance) a cluster made of 4-core nodes, and a single-threaded task (e.g. samtools), are the other 3 cores just going to waste or will the scheduler allocate multiple single-threaded jobs to one node? I've cc'd galaxy-dev instead of galaxy-user as I think the conversation has gone that way! Thanks again, Clare On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks wrote: > >> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks >> wrote: >> >>> Scalability issues are more likely to arise on the back end than the front >>> end, so you'll want to ensure that you have enough compute nodes. BWA uses >>> four nodes by default--Enis, does the cloud config change this >>> parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to >>> be able to run a BWA job simultaneously. >>> >> >> Actually, one other question - this paragraph makes me realise that I >> don't really understand how Galaxy is distributing jobs. I had thought >> that each job would only use one node, and in some cases take >> advantage of multiple cores within that node. I'm taking a "node" to >> be a set of cores with their own shared memory, so in this case a VM >> instance, is this right? If some types of jobs can be distributed over >> multiple nodes, can I configure, in Galaxy, how many nodes they should >> use? > > You're right -- my word choices were poor. Replace 'node' with 'core' in my > paragraph to get an accurate suggestion for resources. > > Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to > different cluster nodes. Jobs that require multiple cores typically run on a > single node. Enis can chime in on whether CloudMan supports job submission > over multiple nodes; this would require setup of an appropriate parallel > environment and a tool that can make use of this environment. > > Good luck, > J. > > > > -- E: s...@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
