Re: [OMPI users] 4.0.5 on Linux Pop!_OS
>> Core(s) per socket: 8 > "4. If none of a hostfile, the --host command line parameter, or an RM is > present, Open MPI defaults to the number of processor cores" Have you tried -np 8? On Sun, Nov 8, 2020 at 12:25 AM Paul Cizmas via users < users@lists.open-mpi.org> wrote: > Gilles: > > Thank you for your reply. Unfortunately, it did not quite help me. > > As I said in my e-mail, I can run this on a Mac by only specifying > > $mympirun -np 12 $exe input1 > > without worrying about “slots”. > > So, my questions are: > > 1. Why do I need “slot” on the Linux? > > 2. Is there a relation between slots, sockets, cores and threads? The > workstation has 1 socket, 8 cores per socket and 2 threads per core, or 16 > CPUs. How many slots are there? > > 3. If I need to specify “slot”, what is the syntax? > > I tried: > > $mympirun -np 12 slots=12 $exe input1 > > and got: > == > No protocol specified > -- > There are not enough slots available in the system to satisfy the 12 > slots that were requested by the application: > > slots=12 > > Either request fewer slots for your application, or make more slots > available for use. > == > Finally, I made it work by using > > $mympirun -np 12 --use-hwthread-cpus $exe input1 > > and ignored all the slot options, so I missed the chance to learn about > slots. > > I did not find an example on how to specify the “slot” although the > message lists four options - four options but zero examples. > > Thank you, > Paul > > > On Nov 7, 2020, at 8:23 PM, Gilles Gouaillardet via users < > users@lists.open-mpi.org> wrote: > > > > Paul, > > > > a "slot" is explicitly defined in the error message you copy/pasted: > > > > "If none of a hostfile, the --host command line parameter, or an RM is > > present, Open MPI defaults to the number of processor cores" > > > > The error message also lists 4 ways on how you can move forward, but > > you should first ask yourself if you really want to run 12 MPI tasks > > on your machine. > > > > Cheers, > > > > Gilles > > > > On Sun, Nov 8, 2020 at 11:14 AM Paul Cizmas via users > > wrote: > >> > >> Hello: > >> > >> I just installed OpenMPI 4.0.5 on a Linux machine running Pop!_OS (made > by System76). The workstation has the following architecture: > >> > >> Architecture:x86_64 > >> CPU op-mode(s): 32-bit, 64-bit > >> Byte Order: Little Endian > >> Address sizes: 39 bits physical, 48 bits virtual > >> CPU(s): 16 > >> On-line CPU(s) list: 0-15 > >> Thread(s) per core: 2 > >> Core(s) per socket: 8 > >> Socket(s): 1 > >> NUMA node(s):1 > >> Vendor ID: GenuineIntel > >> CPU family: 6 > >> > >> I am trying to run on the Linux box a code that I usually run on a Mac > OS without any issues. > >> > >> The script that I use is: > >> > >> exe='/usr/bin/mycode' # on jp2 > >> mympirun='/opt/openmpi/4.0.5/bin/mpirun' # GFortran on jp2 > >> $mympirun -np 12 $exe input1 > >> > >> I get the following error: > >> > >> No protocol specified > >> > -- > >> There are not enough slots available in the system to satisfy the 12 > >> slots that were requested by the application: > >> > >> /usr/bin/mycode > >> > >> Either request fewer slots for your application, or make more slots > >> available for use. > >> > >> A "slot" is the Open MPI term for an allocatable unit where we can > >> launch a process. The number of slots available are defined by the > >> environment in which Open MPI processes are run: > >> > >> 1. Hostfile, via "slots=N" clauses (N defaults to number of > >>processor cores if not provided) > >> 2. The --host command line parameter, via a ":N" suffix on the > >>hostname (N defaults to 1 if not provided) > >> 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.) > >> 4. If none of a hostfile, the --host command line parameter, or an > >>RM is present, Open MPI defaults to the number of processor cores > >> > >> In all the above cases, if you want Open MPI to default to the number > >> of hardware threads instead of the number of processor cores, use the > >> --use-hwthread-cpus option. > >> > >> Alternatively, you can use the --oversubscribe option to ignore the > >> number of available slots when deciding the number of processes to > >> launch. > >> === > >> > >> I do not understand “slots”. The architecture description of my Linux > box lists sockets, cores and threads, but not slots. > >> > >> What shall I specify instead of "-np 12”? >
Re: [OMPI users] 4.0.5 on Linux Pop!_OS
Gilles: Thank you for your reply. Unfortunately, it did not quite help me. As I said in my e-mail, I can run this on a Mac by only specifying $mympirun -np 12 $exe input1 without worrying about “slots”. So, my questions are: 1. Why do I need “slot” on the Linux? 2. Is there a relation between slots, sockets, cores and threads? The workstation has 1 socket, 8 cores per socket and 2 threads per core, or 16 CPUs. How many slots are there? 3. If I need to specify “slot”, what is the syntax? I tried: $mympirun -np 12 slots=12 $exe input1 and got: == No protocol specified -- There are not enough slots available in the system to satisfy the 12 slots that were requested by the application: slots=12 Either request fewer slots for your application, or make more slots available for use. == Finally, I made it work by using $mympirun -np 12 --use-hwthread-cpus $exe input1 and ignored all the slot options, so I missed the chance to learn about slots. I did not find an example on how to specify the “slot” although the message lists four options - four options but zero examples. Thank you, Paul > On Nov 7, 2020, at 8:23 PM, Gilles Gouaillardet via users > wrote: > > Paul, > > a "slot" is explicitly defined in the error message you copy/pasted: > > "If none of a hostfile, the --host command line parameter, or an RM is > present, Open MPI defaults to the number of processor cores" > > The error message also lists 4 ways on how you can move forward, but > you should first ask yourself if you really want to run 12 MPI tasks > on your machine. > > Cheers, > > Gilles > > On Sun, Nov 8, 2020 at 11:14 AM Paul Cizmas via users > wrote: >> >> Hello: >> >> I just installed OpenMPI 4.0.5 on a Linux machine running Pop!_OS (made by >> System76). The workstation has the following architecture: >> >> Architecture:x86_64 >> CPU op-mode(s): 32-bit, 64-bit >> Byte Order: Little Endian >> Address sizes: 39 bits physical, 48 bits virtual >> CPU(s): 16 >> On-line CPU(s) list: 0-15 >> Thread(s) per core: 2 >> Core(s) per socket: 8 >> Socket(s): 1 >> NUMA node(s):1 >> Vendor ID: GenuineIntel >> CPU family: 6 >> >> I am trying to run on the Linux box a code that I usually run on a Mac OS >> without any issues. >> >> The script that I use is: >> >> exe='/usr/bin/mycode' # on jp2 >> mympirun='/opt/openmpi/4.0.5/bin/mpirun' # GFortran on jp2 >> $mympirun -np 12 $exe input1 >> >> I get the following error: >> >> No protocol specified >> -- >> There are not enough slots available in the system to satisfy the 12 >> slots that were requested by the application: >> >> /usr/bin/mycode >> >> Either request fewer slots for your application, or make more slots >> available for use. >> >> A "slot" is the Open MPI term for an allocatable unit where we can >> launch a process. The number of slots available are defined by the >> environment in which Open MPI processes are run: >> >> 1. Hostfile, via "slots=N" clauses (N defaults to number of >>processor cores if not provided) >> 2. The --host command line parameter, via a ":N" suffix on the >>hostname (N defaults to 1 if not provided) >> 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.) >> 4. If none of a hostfile, the --host command line parameter, or an >>RM is present, Open MPI defaults to the number of processor cores >> >> In all the above cases, if you want Open MPI to default to the number >> of hardware threads instead of the number of processor cores, use the >> --use-hwthread-cpus option. >> >> Alternatively, you can use the --oversubscribe option to ignore the >> number of available slots when deciding the number of processes to >> launch. >> === >> >> I do not understand “slots”. The architecture description of my Linux box >> lists sockets, cores and threads, but not slots. >> >> What shall I specify instead of "-np 12”? >> >> Thank you, >> Paul
Re: [OMPI users] 4.0.5 on Linux Pop!_OS
Paul, a "slot" is explicitly defined in the error message you copy/pasted: "If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores" The error message also lists 4 ways on how you can move forward, but you should first ask yourself if you really want to run 12 MPI tasks on your machine. Cheers, Gilles On Sun, Nov 8, 2020 at 11:14 AM Paul Cizmas via users wrote: > > Hello: > > I just installed OpenMPI 4.0.5 on a Linux machine running Pop!_OS (made by > System76). The workstation has the following architecture: > > Architecture:x86_64 > CPU op-mode(s): 32-bit, 64-bit > Byte Order: Little Endian > Address sizes: 39 bits physical, 48 bits virtual > CPU(s): 16 > On-line CPU(s) list: 0-15 > Thread(s) per core: 2 > Core(s) per socket: 8 > Socket(s): 1 > NUMA node(s):1 > Vendor ID: GenuineIntel > CPU family: 6 > > I am trying to run on the Linux box a code that I usually run on a Mac OS > without any issues. > > The script that I use is: > > exe='/usr/bin/mycode' # on jp2 > mympirun='/opt/openmpi/4.0.5/bin/mpirun' # GFortran on jp2 > $mympirun -np 12 $exe input1 > > I get the following error: > > No protocol specified > -- > There are not enough slots available in the system to satisfy the 12 > slots that were requested by the application: > > /usr/bin/mycode > > Either request fewer slots for your application, or make more slots > available for use. > > A "slot" is the Open MPI term for an allocatable unit where we can > launch a process. The number of slots available are defined by the > environment in which Open MPI processes are run: > > 1. Hostfile, via "slots=N" clauses (N defaults to number of > processor cores if not provided) > 2. The --host command line parameter, via a ":N" suffix on the > hostname (N defaults to 1 if not provided) > 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.) > 4. If none of a hostfile, the --host command line parameter, or an > RM is present, Open MPI defaults to the number of processor cores > > In all the above cases, if you want Open MPI to default to the number > of hardware threads instead of the number of processor cores, use the > --use-hwthread-cpus option. > > Alternatively, you can use the --oversubscribe option to ignore the > number of available slots when deciding the number of processes to > launch. > === > > I do not understand “slots”. The architecture description of my Linux box > lists sockets, cores and threads, but not slots. > > What shall I specify instead of "-np 12”? > > Thank you, > Paul
[OMPI users] 4.0.5 on Linux Pop!_OS
Hello: I just installed OpenMPI 4.0.5 on a Linux machine running Pop!_OS (made by System76). The workstation has the following architecture: Architecture:x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian Address sizes: 39 bits physical, 48 bits virtual CPU(s): 16 On-line CPU(s) list: 0-15 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 1 NUMA node(s):1 Vendor ID: GenuineIntel CPU family: 6 I am trying to run on the Linux box a code that I usually run on a Mac OS without any issues. The script that I use is: exe='/usr/bin/mycode' # on jp2 mympirun='/opt/openmpi/4.0.5/bin/mpirun' # GFortran on jp2 $mympirun -np 12 $exe input1 I get the following error: No protocol specified -- There are not enough slots available in the system to satisfy the 12 slots that were requested by the application: /usr/bin/mycode Either request fewer slots for your application, or make more slots available for use. A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run: 1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided) 2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided) 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.) 4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option. Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch. === I do not understand “slots”. The architecture description of my Linux box lists sockets, cores and threads, but not slots. What shall I specify instead of "-np 12”? Thank you, Paul