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MVAPICH2 1.0.3 User Guide
MVAPICH Team Last revised: July 2, 2008 |
InfiniBand and 10GbE/iWARP are emerging as high-performance interconnects delivering low latency and high bandwidth. They are also getting widespread acceptance due to their open standards.
MVAPICH (pronounced as “em-vah-pich”) is an open-source MPI software to exploit the novel features and mechanisms of InfiniBand, iWARP and other RDMA-enabled interconnects and deliver best performance and scalability to MPI applications. This software is developed in the Network-Based Computing Laboratory (NBCL), headed by Prof. Dhabaleswar K. (DK) Panda.
Currently, there are two versions of this MPI: MVAPICH with MPI-1 semantics and MVAPICH2 with MPI-2 semantics. This open-source MPI software project started in 2001 and a first high-performance implementation was demonstrated at Supercomputing ’02 conference. After that, this software has been steadily gaining acceptance in the HPC and InfiniBand community. As of June 10th, 2008, more than 700 organizations (National Labs, Universities and Industry) world-wide have downloaded this software from OSU’s web site directly. In addition, many InfiniBand and iWARP vendors, server vendors, and systems integrators have been incorporating MVAPICH/MVAPICH2 into their software stacks and distributing it. Several InfiniBand systems using MVAPICH/MVAPICH2 have obtained positions in the TOP 500 ranking. MVAPICH and MVAPICH2 are also available with the Open Fabrics Enterprise Distribution (OFED) stack. Both MVAPICH and MVAPICH2 distributions are available under BSD licensing.
More details on MVAPICH/MVAPICH2 software, users list, mailing lists, sample performance numbers on a wide range of platforms and interconnect, a set of OSU benchmarks, related publications, and other InfiniBand- and iWARP-related projects (parallel file systems, storage, data centers) can be obtained from the following URL:
http://mvapich.cse.ohio-state.edu
This document contains necessary information for MVAPICH2 users to download, install, test, use, tune and troubleshoot MVAPICH2 1.0.3. As we get feedbacks from users and take care of bug-fixes, we introduce new tarballs and also continuously update this document. Thus, we strongly request you to refer to our web page for updates.
This guide is designed to take the user through all the steps involved in configuring, installing, running and tuning MPI applications over InfiniBand using MVAPICH2 1.0.3.
In Section 3 we describe all the features in MVAPICH2 1.0.3. As you read through this section, please note our new features (highlighted as NEW) in the 1.0 series. Some of these features are designed in order to optimize specific type of MPI applications and achieve greater scalability. Section 4 describes in detail the configuration and installation steps. This section enables the user to identify specific compilation flags which can be used to turn some of the features on of off. Basic usage of MVAPICH2 is explained in Section 5. Section 6 provides instructions for running MVAPICH2 with some of the advanced features. Section 7 describes the usage of the OSU Benchmarks. If you have any problems using MVAPICH2, please check Section 8 where we list some of the common problems people face. In Section 9 we suggest some tuning techniques for multi-thousand node clusters using some of our new features. Finally in Section 10 we list all important run-time parameters, their default values and a small description of what that parameter stands for.
MVAPICH2 (MPI-2 over InfiniBand) is an MPI-2 implementation based on MPICH2 ADI3 layer. It also supports all MPI-1 functionalities. MVAPICH2 1.0.3 is available as a single integrated package (with MPICH2 1.0.5p4).
The current release supports the following five underlying transport interfaces:
MVAPICH2-1.0.3 delivers the same level of performance as MVAPICH 1.0.1, the latest release package of MVAPICH supporting MPI-1 standard. In addition, MVAPICH2 1.0.3 provides support and optimizations for other MPI-2 features, multi-threading and fault-tolerance (Checkpoint-restart).
A complete set of features of MVAPICH2 1.0.3 are:
Available for all interfaces.
This uDAPL support is generic and can work with other networks that provide uDAPL interface. Please note that the stability and performance of MVAPICH2 with uDAPL depends on the stability and performance of the uDAPL library used. Starting from version 1.0.3, MVAPICH2 supports both uDAPL v2 and v1.2 on Linux.
The MVAPICH2 1.0.3 package and the project also includes the following provisions:
The MVAPICH2 1.0.3 source code package includes the MPICH2 1.0.5p4 version. All the required files are present as a single tarball.
You can go to the MVAPICH2 website to obtain the source code.
Untar the archive you have downloaded from the web page. Given 1.0.3 version, the following command can run on most Unix machines:
$ tar xzf mvapich2-1.0.3.tar.gz
You will have a directory named mvapich2-1.0.3.
The MVAPICH2 source code is also available for download through a public SVN:
https://mvapich.cse.ohio-state.edu/svn/mpi/mvapich2
There are several options to build MVAPICH2 1.0.3 based on the underlying InfiniBand libraries you want to utilize. In this section we describe in detail the steps you need to perform to correctly build MVAPICH2 on your choice of libraries, namely OpenFabrics Gen2-IB, OpenFabrics Gen2-iWARP, Mellanox VAPI, uDAPL and TCP/IP.
There are several methods to configure MVAPICH2 and optimize it for a given platform.
Go to the mvapich2-1.0.3 directory. We have included a single script for Gen2
(make.mvapich2.ofa) that takes care of different platforms, compilers and architectures. By
default, the compilation script uses gcc. In order to use a specific compiler, set the CC, CXX,
F77, and F90 variables to the appropriate commands. MVAPICH2 currently supports the
GCC, Intel, PathScale and PGI compiler suites for Gen2.
MVAPICH2 has many optimization schemes to enhance performance. In 1.0.3, many of those optimization schemes can be turned on/off by runtime variables. Please refer to Section 6.2 for examples to run MVAPICH2 with those runtime variables and Section 10 for a full list of the variables controlling other optimization schemes. However, for performance reasons, there are still some schemes controlled by compilation flags which are listed in the variable CFLAGS (in the default compilation script) and/or various configure options.
After setting all the parameters, the script make.mvapich2.ofa configures, builds and installs the entire package in the directory specified by the variable PREFIX.
There are several methods to configure MVAPICH2 and optimize it for a given platform.
Go to the mvapich2-1.0.3 directory. We have provided a single script make.mvapich2.udapl for building over uDAPL.
Because there are many varieties of uDAPL packages, the script make.mvapich2.udapl requires two parameters: dat_library_path and dat_include_path, before it can start building the package.
By default, the compilation script uses gcc. In order to use a specific compiler, set the CC, CXX, F77, and F90 variables to the appropriate commands. MVAPICH2 currently supports the GCC, Intel, PathScale, PGI, and Sun Studio compiler suites for uDAPL. In addition, it may prompt for options, such as cluster size, IO bus and link speed. The script then proceeds to configure, build and install the package.
MVAPICH2 has many optimization schemes to enhance performance. These schemes can be turned on/off by the compilation flags which are listed in the variable CFLAGS (in the default compilation script) and/or various configure options.
After setting all the parameters, the script make.mvapich2.udapl configures, builds and installs the entire package in the directory specified by the variable PREFIX.
There are several methods to configure MVAPICH2 and optimize it for a given platform.
Go to the mvapich2-1.0.3 directory. We have included a single script for VAPI
(make.mvapich2.vapi) that takes care of different platforms, compilers and architectures.
By default, the compilation script uses gcc. In order to use a specific compiler, set the CC,
CXX, F77, and F90 variables to the appropriate commands. MVAPICH2 currently supports
the GCC, Intel, PathScale and PGI compiler suites for VAPI. The platform/architecture is
detected automatically. The script prompts the user for parameters like I/O Bus type (PCI-X,
PCI-Ex) and InfiniBand link speed (SDR, DDR).
After setting all the parameters, the script make.mvapich2.vapi configures, builds and installs the entire package in the directory specified by the variable PREFIX.
Go to the mvapich2-1.0.3 directory. We have provided a script make.mvapich2.tcp for building MVAPICH2 over TCP/IP intended for use over IPoIB (IP over InfiniBand). By default, the compilation script uses gcc. In order to use a specific compiler, set the CC, CXX, F77, and F90 variables to the appropriate commands. MVAPICH2 currently supports the GCC, Intel, PathScale, PGI, and Sun Studio compiler suites for TCP/IPoIB. Simply execute this script (e.g. ./make.mvapich2.tcp) for completing your build.
MVAPICH2 provides a variety of MPI compilers to support applications written in different programming languages. Please use mpicc, mpif77, mpiCC, or mpif90 to compile applications. The correct compiler should be selected depending upon the programming language of your MPI application.
These compilers are available in the MVAPICH2_HOME/bin directory. MVAPICH2 installation directory can also be specified by modifying $PREFIX, then all the above compilers will also be present in the $PREFIX/bin directory.
Prerequisites: ssh should be enabled between the front nodes and the computing nodes.
Please follow these steps to setup MPD:
$ export MPD_BIN=$MVAPICH2_HOME/bin
$ export PATH=$MVAPICH2_HOME/bin:$PATH
$MVAPICH2_HOME is the installation path of your MVAPICH2, as specified by $PREFIX when you configure MVAPICH2.
Specify the hostnames of the compute nodes in a file. If you have a hostfile like:
n0
n1
n2
n3
then one process per node will be started on each one of these compute nodes.
$ mpdboot -n 4 -f hostfile
Note: The command, mpdboot, also takes a default hostfile name mpd.hosts. If you have created the hostfile as mpd.hosts, you can omit the option “-f hostfile”.
$ mpdtrace
This should list all the nodes specified in the hostfile, not necessarily in the order specified in the hostfile.
Up to now, we have specified setting up the environment, which is independent of the underlying device supported by MVAPICH2. In the next sections, we present details specific to different devices.
To start multiple processes, mpiexec can be used in the following fashion:
$ mpiexec -n 4 ./cpi
Four processes will be started on the compute nodes n0, n1, n2 and n3. mpiexec can also be run with several options. $ mpiexec --help lists all the possible options. A useful option is to specify a machinefile which holds the process mapping to machines. It can also be used to specify the number of processes to be run on each host. The machinefile option can be used with mpiexec as follows:
$ mpiexec -machinefile mf -n 4 ./cpi
where the machine file ”mf” contains the process to machine mapping. For example, if you want to run all the 4 processes on n0, then ”mf” contains the following lines:
$ cat mf
n0
n0
n0
n0
Environmental variables can be set with mpiexec as follows:
$ mpiexec -n 4 -env ENV1 value1 -env ENV2 value2 ./cpi
Note that the environmental variables should be put immediately before the executable file. The mpiexec command also propagates exported variables in its runtime environment to all processes by default. Exporting a variable before running mpiexec has the same effect as explicitly passing its value with the -env command line option. The command above could be done in the following manner when using a Bourne shell derivative:
$ export ENV1=value1
$ export ENV2=value2
$ mpiexec -n 4 ./cpi
MVAPICH2 provides shared library support. This feature allows you to build your application on top of MPI shared library. If you choose this option, you still will be able to compile applications with static libraries. But as default, when you have shared library support enabled your applications will be built on top of shared libraries automatically. the following commands provide some examples of how to build and run your application with shared library support.
MVAPICH2 provides TotalView support. The following commands provide an example of how to build and run your application with TotalView support. Note: running TotalView requires correct setup in your environment, if you encounter any problem with your setup, please check with your system administrator for help.
In MVAPICH2, Gen2-iWARP support is enabled with the use of the run time environment variable ‘‘MV2_USE_IWARP_MODE’’.
In addition to this flag, all the systems to be used need the following one time setup for enabling RDMA CM usage.
Programs can be executed as follows:
$ mpiexec -n 4 -env MV2_USE_IWARP_MODE 1 -env ENV1 value1 prog
The iWARP device also provides totalview debugging and shared library support. Please refer to section 5.3.1 and 5.3.2 for shared library and totalview support, respectively.
MVAPICH2 can be configured with the uDAPL device, as described in the section 4.4.2 . To compile MPI applications, please refer to the section 5.1. In order to run MPI applications with uDAPL support, please specify the environmental variable MV2_DAPL_PROVIDER. As an example,
$ mpiexec -n 4 -env MV2_DAPL_PROVIDER ib0 ./cpi
or:
$ export MV2_DAPL_PROVIDER=ib0
$ mpiexec -n 4 ./cpi
Please check the /etc/dat.conf file to find all the available uDAPL service providers. The default value for the uDAPL provider will be chosen, if no environment variable is provided at runtime. For OFED 1.2, please use OpenIB-cma as the uDAPL provider.
The uDAPL device also provides totalview debugging and shared library support. Please refer to section 5.3.1 and 5.3.2 for shared library and totalview support, respectively.
If you would like to run an MPI job using IPoIB but your IB card is not the default interface for ip traffic you have two options. For both of the options , assume that you have a cluster setup as the following:
|
In this scenario, you will start up mpd like normal. However, you will need to create a machine file for
mpiexec that tells mpiexec to use a particular interface. Example:
$ cat - > $(MPD_HOSTFILE) compute1
compute2
compute3
compute4
$ mpdboot -n 4 -f $(MPD_HOSTFILE)
compute1 ifhn=192.168.1.1
compute2 ifhn=192.168.1.2
compute3 ifhn=192.168.1.3
compute4 ifhn=192.168.1.4
The ifhn portion tells mpiexec to use the interface associated with that ip address for
each machine. You can now run your MPI application using IPoIB similar to the following.
$ mpiexec -n $(NUM_PROCESS) -f $(MACHINE_FILE) $(MPI_APPLICATION)
In this scenario you will start up mpd in a modified fashion. However, you will not need to create a
machine file for mpiexec. Your hostsfile for mpdboot must contain the ip addresses, or hostnames mapped
to these addresses, of each machine’s IPoIB interface. The only exception is that you do not list the ip
address or hostname of the local machine. This will be specified on the command line of the mpdboot
command using the –ifhn option. Example:
$ cat - > $(MPD_HOSTFILE)
192.168.1.2
192.168.1.3
192.168.1.4
$ mpdboot -n 4 -f $HOSTSFILE --ifhn=192.168.1.1
The –ifhn option tells mpdboot to use the interface corresponding to that ip address to create the mpd
ring and run MPI jobs. You can now run your MPI application using IPoIB similar to the following.
$ mpiexec -n $(NUM_PROCES) $(MPI_APPLICATION)
Note: For both options, you can replace the IPoIB addresses with aliases
SLURM is an open-source resource manager designed by Lawrence Livermore National Laboratory.
SLURM software package and its related documents can be downloaded from:
http://www.llnl.gov/linux/slurm/
Once SLURM is installed and the daemons are started, applications compiled with MVAPICH2 can be launched by SLURM, e.g.
$ srun -n2 --mpi=none ./a.out
The use of SLURM enables many good features such as explicit CPU and memory binding. For example, if you have two processes and want to bind the first process to CPU 0 and Memory 0, and the second process to CPU 4 and Memory 1, then it can be achieved by:
$ srun --cpu_bind=v,map_cpu:0,4 --mem_bind=v,map_mem:0,1 -n2 --mpi=none ./a.out
For more information about SLURM and its features please visit SLURM website.
In this section, we present the usage instructions for advanced features provided by MVAPICH2.
MVAPICH2 has integrated multi-rail support. Run-time variables are used to specify the control
parameters of the multi-rail support; number of adapters with MV2_NUM_HCAS (section 10.18), number
of ports per adapter with MV2_NUM_PORTS (section 10.19), and number of queue pairs per port with
MV2_NUM_QP_PER_PORT (section 10.20). Those variables are default to 1 if you do not specify them.
Following is an example to run multi-rail support with two adapters, using one port per adapter and one
queue pair per port:
$ mpiexec -n 2 -env MV2_NUM_HCAS 2 -env MV2_NUM_PORTS 1 -env MV2_NUM_QP_PER_PORT 1
prog
Note that you don’t need to put -env MV2_NUM_PORTS 1 -env MV2_NUM_QP_PER_PORT 1 since they
default to 1, so you can type:
$ mpiexec -n 2 -env MV2_NUM_HCAS 2 prog
In MVAPICH2-1.0.3, run-time variables are used to switch various optimization schemes on and off. Following is a list of optimizations schemes and the control environmental variables, for a full list please refer to the section 10:
MVAPICH2 provides system-level checkpoint/restart functionality for the OpenFabrics Gen2-IB interface. Three methods are provided to invoke checkpointing: Manual, Automated and Application Initiated Synchronous Checkpointing. In order to utilize the checkpoint/restart functionality there a couple of steps that need to be followed.
And users are strongly encouraged to read the Administrators guide of BLCR, and test the BLCR on the target platform, before using the checkpointing feature of MVAPICH2.
Now, your system is set up to use the Checkpoint/Restart features of MVAPICH2. There are several parameters related to MVAPICH2 to be setup to control the configuration and useage of this feature.
In order to provide maximum flexibility to end users who wish to use the checkpoint/restart features of MVAPICH2, we’ve provided three different methods which can be used to take the checkpoints during the execution of the MPI application. These methods are described as follows:
#include "mpi.h"
#include <unistd.h> #include <stdio.h> int main(int argc,char *argv[]) { MPI_Init(&argc,&argv); printf("Computation\n"); sleep(5); MPI_Barrier(MPI_COMM_WORLD); MVAPICH2_Sync_Checkpoint(); MPI_Barrier(MPI_COMM_WORLD); printf("Computation\n"); sleep(5); MPI_Finalize(); return 0; } |
To restart a job from a checkpoint, users need to issue another command of BLCR, ‘‘cr_restart’’ with the checkpoint file name of the MPI job console as the parameter, usually context.<pid>. The checkpoint file name of the MPI job console can be specified when issuing the checkpoint, see the ‘‘cr_checkpoint --help’’ for more information. Please note that the names of checkpoint files of the MPI processes will be assigned according to the environment variable MV2_CKPT_FILE, ($MV2_CKPT_FILE.<number of checkpoint>.<process rank>).
Please refer to the Section 8.7 for troubleshooting with Checkpoint/Restart.
In MVAPICH2, for using RDMA CM the runtime variable MV2_USE_RDMA_CM needs to be used as described in 10. (Note: In order to use RDMA CM support on OFED 1.1 software stack, please add the flag -DOFED_VERSION_1_1 to the cflags in the compilation script make.mvapich2.ofa)
In addition to these flags, all the systems to be used need the following one time setup for enabling RDMA CM usage.
Programs can be executed as follows:
$ mpiexec -n 2 -env MV2_USE_RDMA_CM 1 prog
In MVAPICH2, support for shared memory based collectives has been enabled for MPI applications running over OpenFabrics Gen2-IB, Gen2-iWARP and uDAPL stack. Currently, this support is available for the following collective operations:
Optionally, these feature can be turned off at runtime by using the following parameters:
Please refer to Section 10 for further details.
MVAPICH2 supports hot-spot and congestion avoidance using InfiniBand multi-pathing mechanism. This support is available for MPI applications using OpebFabrics stack and InfiniBand adapters.
To enable this functionality, a run-time variable, MV2_USE_HSAM (Section 10.37) can be enabled, as shown in the following example:
$ mpiexec -n 2 -env MV2_USE_HSAM 1 ./cpi
This functionality automatically defines the number of paths for hot-spot avoidance. Alternatively, the maximum number of paths to be used between a pair of processes can be defined by using a run-time variable MV2_NUM_QP_PER_PORT (Section 10.20).
We expect this functionality to show benefits in the presence of at least partially non-overlapping paths in the network. OpenSM, the subnet manager distributed with OpenFabrics supports LMC mechanism, which can be used to create multiple paths:
$ opensm -l4
will start the subnet manager with LMC value to four, creating sixteen paths between every pair of nodes.
MVAPICH2 supports network fault recovery by using InfiniBand Automatic Path Migration mechanism. This support is available for MPI applications using OpebFabrics stack and InfiniBand adapters.
To enable this functionality, a run-time variable, MV2_USE_APM (section 10.33) can be enabled, as shown in the following example:
$ mpiexec -n 2 -env MV2_USE_APM 1 ./cpi
MVAPICH2 also supports testing Automatic Path Migration in the subnet in the absence of network faults. This can be controlled by using a run-time variable MV2_USE_APM_TEST (section 10.34). This should be combined with MV2_USE_APM as follows:
$ mpiexec -n 2 -env MV2_USE_APM 1 -env MV2_USE_APM_TEST 1./cpi
If you have arrived at this point, you have successfully installed MVAPICH2. Congratulations!! In the mvapich2-1.0.3/osu_benchmarks directory, we provide these basic performance tests:
These benchmarks are also available on our project’s web page. Sample performance numbers for these benchmarks on representative platforms with InfiniBand and iWARP adapters are also included on our projects’ web page. You are welcome to compare your performance numbers with our numbers. If you see any big discrepancy, please let us know by sending an email to mvapich-discuss@cse.ohio-state.edu.
Based on our experience and feedback we have received from our users, here we include some of the problems a user may experience and the steps to resolve them. If you are experiencing any other problem, please feel free to contact us by sending an email to mvapich-discuss@cse.ohio-state.edu.
MVAPICH2 can be used over five underlying transport interfaces, namely OpenFabrics (Gen2), OpenFabrics (Gen2-iWARP), VAPI, UDAPL and TCP/IP. Based on the underlying library being utilized, the troubleshooting steps may be different. However, some of the troubleshooting hints are common for all underlying libraries. Thus, in this section, we have divided the troubleshooting tips into four sections: General troubleshooting and Troubleshooting over any one of the five transport interfaces.
This is a problem which typically occurs due to the presence of multiple installations of MVAPICH2 on the same set of nodes. The problem is due to the presence of mpi.h other than the one, which is used for executing the program. This problem can be resolved by making sure that the mpi.h from other installation is not included.
fork() and system() is supported for the OpenFabrics device as long as the kernel is being used is Linux 2.6.16 or newer. Additionally, the version of OFED used should be 1.2 or higher. The environment variable IBV_FORK_SAFE=1 must also be set to enable fork support.
There is a known bug with the PathScale compiler (before version 2.5) when building MVAPICH2. This problem will be solved in the next major release of the PathScale compiler. To work around this bug, use the the “-LNO:simd=0” C compiler option. This can be set in the build script similarly to:
export CC=‘‘pathcc -LNO:simd=0’’
Please note the use of double quotes. If you are building shared libraries and are using the PathScale compiler (version below 2.5), then you should add “-g” to your CFLAGS, in order to get around a compiler bug.
If you get this error, please set your .mpd.conf and .mpdpasswd files.
MVAPICH2 supports CPU affinity for multi-way SMP systems. This feature requires a kernel version of 2.6 The above error reports that CPU affinity cannot be enabled on the system. This feature can be disabled by setting -env MV2_ENABLE_AFFINITY 0.
MVAPICH2 uses CPU affinity to have better performance for single-threaded programs. For multi-threaded programs, however, it may schedule all the threads of a process to run on the same CPU. CPU affinity should be disabled in this case to solve the problem, i.e. set -env MV2_ENABLE_AFFINITY 0.
MPI programs built with gfortran might not appear to run correctly due to the default output buffering
used by gfortran. If it seems there is an issue with program output, the GFORTRAN_UNBUFFERED_ALL
variable can be set to “y” and exported into the environment before using the mpiexec command to
launch the program, as done in the bash shell example below:
$ export GFORTRAN_UNBUFFERED_ALL=y
The above error reports that the InfiniBand Adapter is not ready for communication. Make sure that the drivers are up. This can be done by executing the following command which gives the path at which drivers are setup.
% locate libibverbs
In order to check the status of the IB link, one of the following commands can be used:
% ibstatus
or
% ibv_devinfo.
Add -DGEN2_OLD_DEVICE_LIST_VERB macro to CFLAGS and rebuild MVAPICH2-gen2. If this happens, this means that your Gen2 installation is old and needs to be updated.
A possible reason could be inability to pin the memory required. Make sure the following parameters are set.
In /etc/security/limits.conf add the following line:
* soft memlock phys_mem_in_KB
After this, add the following line to /etc/init.d/sshd and restart sshd
ulimit -l phys_mem_in_KB
HSAM functionality uses multi-pathing mechanism with LMC functionality. However, some versions of OpenFabrics Drivers (including OpenFabrics Enterprise Distribution (OFED) 1.1) and using the Up*/Down* routing engine do not configure the routes correctly using the LMC mechanism. We strongly suggest to upgrade to OFED 1.2, which supports Up*/Down* routing engine and LMC mechanism correctly.
MVAPICH2 provides network fault tolerance with Automatic Path Migration (APM). However, APM is supported only with OFED 1.2 onwards. With OFED 1.1 and prior versions of OpenFabrics drivers, APM functionality is not completely supported. Please refer to Section 10.33 and section 10.34
If you configure MVAPICH2 with RDMA_CM and see this error, you need to verify if you have setup up the local IP address to be used by RDMA_CM in the file /etc/mv2.conf. Further, you need to make sure that this file has the appropriate file read permissions. Please follow Section 6.4 for more details on this.
If you get this error, please verify that the IP address specified /etc/mv2.conf is correctly specified with the IP address of the device you plan to use RDMA_CM with.
If see this error, you need to check whether the specified network is working or not.
If you configure MVAPICH2 with RDMA_CM and see this error, you need to verify if you have setup up the local IP address to be used by RDMA_CM in the file /etc/mv2.conf. Further, you need to make sure that this file has the appropriate file read permissions. Please follow Section 5.4 for more details on this.
If you get this error, please verify that the IP address specified /etc/mv2.conf is correctly specified with the IP address of the device you plan to use RDMA_CM with.
If see this error, you need to check whether the specified network is working or not.
If your MPI application cannot pass MPI_Init, please make sure of the following things:
The above error reports that the InfiniBand Adapter is not ready for communication. Make sure that the drivers are up. This can be done by executing
$ locate libvapi
which gives the path at which drivers are setup.
This error is generated during compilation, if the correct path to the InfiniBand library installation is not given.
Please setup the environment variable MTHOME as
/usr/local/ibgd/driver/infinihost
Please setup the environment variable MTHOME as
$ export MTHOME=/usr/local/ibgd/driver/infinihost
If the problem persists, please contact your system administrator or send an email to mvapich-discuss@cse.ohio-state.edu.
This error usually indicates that all InfiniBand links the MPI application is trying to use are not in the PORT_ACTIVE state. Please make sure that all ports show PORT_ACTIVE with the VAPI utility vstat.
Please make sure that the environmental variable "MAC_OSX" is set before your configuration. If you use manual configuration and not make.mvapich2.vapi, you must configure MVAPICH2 in the following way:
% export MAC_OSX=yes % ./configure ..with option.. % make % make install
If you encounter this problem compiling your own applications,
"ld: multiple definitions of symbol _calloc
/usr/lib/libm.dylib(malloc.So) definition of _calloc
/tmp/mvapich2-0.9.3/lib/libmpich.a(dreg-g5.o)
definition of _calloc in section (__TEXT,__text)
ld: multiple definitions of symbol _free
/usr/lib/libm.dylib(malloc.So) definition of _free
/tmp/mvapich2-0.9.3/mvapich/lib/libmpich.a(dreg-g5.o)
definition of _free in section (__TEXT,__text) "
it is likely that you have explicitly included "-lm". You should remove that.
To enable Fortran support, you would need to install the IBM compiler located at (there is a 60-day free trial version) available from IBM.
Once you unpack the tarball, you can customize and use make.mvapich2.vapi to compile and install the package or manually configure, compile and install the package.
If you configure MVAPICH2 with uDAPL and see this error, you need to check whether you have specified the correct uDAPL service provider (at the end of Section 5.3). If you have specified the uDAPL provider but still see this error, you need to check whether the specified network is working or not. For OFED 1.2, please use OpenIB-cma as the uDAPL provider.
If you configure MVAPICH2 with uDAPL and see this error, you need to reduce the value of the environmental variable RDMA_DEFAULT_MAX_WQE depending on the underlying network.
If you get the error: “error while loading shared libraries, libdat.so”, The location of the dat shared library is incorrect. You need to find the correct path of libdat.so and export LD_LIBRARY_PATH to this correct location. For example:
$ export LD_LIBRARY_PATH=/path/to/libdat.so:$LD_LIBRARY_PATH
$ mpiexec -n 2 ./a.out
If you get this error, please set your .mpd.conf and .mpdpasswd files as mentioned in Section 5.3.
This failure may be an indication that there is a problem with your cluster configuration. If you are confident in the correctness of your cluster configuration, then you can tune the timeout with MV2_MPD_RECVTIMEOUT_MULTIPLIER.
Please make sure the following things for a successful restart:
The following things can cause a restart to fail:
FAQ regarding Berkeley Lab Checkpoint/Restart (BLCR) can be found at
http://upc-bugs.lbl.gov/blcr/doc/html/FAQ.html And the userguide for BLCR can be found at
http://upc-bugs.lbl.gov/blcr/doc/html/BLCR_Users_Guide.html
If you encounter any problem with the Checkpoint/Restart support, please feel free to contact us as mvapich-discuss@cse.ohio-state.edu.
MVAPICH2 provides many different parameters for tuning performance for a wide variety of platforms and applications. These parameters can be either compile time parameters or runtime parameters. please refer to Section 9 for a complete description of all these parameters. In this section we classify these parameters depending on what you are tuning for and provide guidelines on how to use them.
The following parameters are important in tuning the memory requirements for adaptive rdma fast path feature.
MV2_RDMA_VBUF_POOL_SIZE is a fixed number of pool of vbufs. These vbufs can be shared among all different connections depending on the communication needs of each connection.
On the other hand, the product of MV2_VBUF_TOTAL_SIZE and MV2_NUM_RDMA_BUFFER generally is a measure of the amount of memory registered for eager message passing. These buffers are not shared across connections.
In MVAPICH2-1.0, MV2_VBUF_TOTAL_SIZE is adjustable by environmental variables. Please refer to Section 10.53 for details.
The main environmental parameters controlling the behavior of the Shared Receive Queue design are:
MV2_SRQ_SIZE is the maximum size of the Shared Receive Queue. You may increase this
to value 1000 if the application requires very large number of processors (4K and beyond).
MV2_SRQ_LIMIT defines the low watermark for the flow control handler. This can be reduced if your aim
is to reduce the number of interrupts.
MVAPICH2 uses shared memory communication channel to achieve high-performance message passing among processes that are on the same physical node. The two main parameters which are used for tuning shared memory performance for small messages are SMPI_LENGTH_QUEUE ( 10.55) and SMP_EAGER_SIZE ( 10.54). The two main parameters which are used for tuning shared memory performance for large messages are SMP_SEND_BUF_SIZE( 10.57) and SMP_NUM_SEND_BUFFER ( 10.56).
SMPI_LENGTH_QUEUE is the size of the shared memory buffer which is used to store outstanding small and control messages. SMP_EAGER_SIZE defines the switch point from Eager protocol to Rendezvous protocol.
Messages larger than SMP_EAGER_SIZE are packetized and sent out in a pipelined manner.
SMP_SEND_BUF_SIZE is the packet size, i.e. the send buffer size. SMP_NUM_SEND_BUFFER is the
number of send buffers.
MVAPICH2 uses on-demand connection management to reduce the memory usage of MPI library. There are 4 parameters to tune connection manager: MV2_ON_DEMAND_THRESHOLD ( 10.22), MV2_CM_RECV_BUFFERS ( 10.7), MV2_CM_TIMEOUT ( 10.9), and MV2_CM_SPIN_COUNT ( 10.8). The first one applies to Gen2-IB, Gen2-iWARP and uDAPL devices and the other three only apply to Gen2 device.
MV2_ON_DEMAND_THRESHOLD defines threshold for enabling on-demand connection management scheme. When the size of the job is larger than the threshold value, on-demand connection management will be used.
MV2_CM_RECV_BUFFERS defines the number of buffers used by connection manager to establish new connections. These buffers are quite small and are shared for all connections, so this value may be increased to 8192 for large clusters to avoid reties in case of packet drops.
MV2_CM_TIMEOUT is the timeout value associated with connection management messages via UD channel. Decreasing this value may lead to faster retries but at the cost of generating duplicate messages.
MV2_CM_SPIN_COUNT is the number of the connection manager polls for new control messages from UD channel for each interrupt. This may be increased to reduce the interrupt overhead when many incoming control messages from UD channel at the same time.
This parameter specifies the path and the base filename for checkpoint files of MPI processes. The checkpoint files will be named as $MV2_CKPT_FILE.<number of checkpoint>.<process rank>, for example, /tmp/ckpt.1.0 is the checkpoint file for process 0’s first checkpoint. To checkpoint on network-based file systems, user just need to specify the path to it, such as /mnt/pvfs2/my_ckpt_file.
This parameter can be used to enable automatic checkpointing. To let MPI job console automatically take checkpoints, this value needs to be set to the desired checkpointing interval. A zero will disable automatic checkpointing. Using automatic checkpointing, the checkpoint file for the MPI job console will be named as $MV2_CKPT_FILE.<number of checkpoint>.auto. Users need to use this file for restart.
This parameter is used to limit the number of checkpoints saved on file system to save the file system space. When set to a positive value N, only the last N checkpoints will be saved.
This parameter specifies the ports of socket connections to pass checkpointing control messages
between MPD manager and MPI process. Users need to have a set of unused ports starting
with $MV2_CKPT_MPD_BASE_PORT on the compute nodes. The used port will be the
$MV2_CKPT_MPD_BASE_PORT + <process rank> for each MPI processes.
This parameter specifies the port of the socket connection for passing checkpointing control messages on MPI
job console node. Users need to have an unused port to be set to
$MV2_CKPT_MPIEXEC_PORT on the console node.
When this parameter is set to any value, the checkpoints will not be required to sync to disk. It can reduce the checkpointing delay in many cases. But if users are using local file system, or any parallel file system with local cache, to store the checkpoints, it is recommended not to set this parameter because otherwise the checkpoint files will be cached in local memory and will likely be lost upon failure.
This defines the number of buffers used by connection manager to establish new connections. These buffers are quite small and are shared for all connections, so this value may be increased to 8192 for large clusters to avoid reties in case of packet drops.
This is the number of the connection manager polls for new control messages from UD channel for each interrupt. This may be increased to reduce the interrupt overhead when many incoming control messages from UD channel at the same time.
This is the timeout value associated with connection management messages via UD channel. Decreasing this value may lead to faster retries but at the cost of generating duplicate messages.
This is to specify the underlying uDAPL library that the user would like to use if MVAPICH2 is built with uDAPL.
The internal MTU used for IB. This parameter should be a string instead of an integer. Valid values are: MTU256, MTU512, MTU1024, MTU2048, MTU4096.
Enable CPU affinity by setting MV2_ENABLE_AFFINITY=1 or disable it by setting
MV2_ENABLE_AFFINITY=0. MV2_ENABLE_AFFINITY does not take effect when _AFFINITY_ is
not defined.
This defines the threshold beyond which the MPI_Get implementation is based on direct one sided RDMA operations.
This specifies the switch point between eager and rendezvous protocol in MVAPICH.
This defines the initial number of pre-posted receive buffers for each connection. If communication happen
for a particular connection, the number of buffers will be increased to
RDMA_PREPOST_DEPTH.
The multiplier to be added to the MPD mpiexec timeout for each process in a job.
This defines the total number of buffers that can be stored in the registration cache. It has no effect if MV2_USE_LAZY_MEM_UNREGISTER is not set. A larger value will lead to less frequent lazy de-registration.
This parameter indicates number of InfiniBand adapters to be used for communication on an end node.
This parameter indicates number of ports per InfiniBand adapter to be used for communication per adapter on an end node.
This parameter indicates number of queue pairs per port to be used for communication on an end node. This is useful in the presence of multiple send/recv engines available per port for data transfer.
The number of RDMA buffers used for the RDMA fast path. This fast path is used to reduce latency and overhead of small data and control messages. This value will be ineffective if MV2_USE_RDMA_FAST_PATH is not set.
This defines threshold for enabling on-demand connection management scheme. When the size of the job is larger than the threshold value, on-demand connection management will be used.
This defines the number of buffers pre-posted for each connection to handle send/receive operations.
This defines the threshold beyond which the MPI_Put implementation is based on direct one sided RDMA operations.
This parameter specifies the arp timeout to be used by RDMA CM module.
The value of this variable can be set to choose different Rendezvous protocols. RPUT (default RDMA-Write) RGET (RDMA Read based), R3 (send/recv based).
The value of this variable controls what message sizes go over the R3 rendezvous protocol. Messages above this message size use MV2_RNDV_PROTOCOL.
The value of this variable controls what message sizes go over the R3 rendezvous protocol when the registration cache is disabled (MV2_USE_LAZY_MEM_UNREGISTER=0). Messages above this message size use MV2_RNDV_PROTOCOL.
This parameter can be used to select the max buffer size of message for shared memory collectives.
This parameter can be used to select the number of communicators using shared memory collectives.
This is the low watermark limit for the Shared Receive Queue. If the number of available work entries on the SRQ drops below this limit, the flow control will be activated.
This is the maximum number of work requests allowed on the Shared Receive Queue.
This parameter is used for recovery from network faults using Automatic Path Migration. This functionality is beneficial in the presence of multiple paths in the network, which can be enabled by using lmc mechanism.
This parameter is used for testing the Automatic Path Migration functionality. It periodically moves the alternate path as the primary path of communication and re-loads another alternate path.
Setting this parameter enables mvapich2 to use blocking mode progress. MPI applications do not take up any CPU when they are waiting for incoming messages.
Setting this parameter enables message coalescing to increase small message throughput
This parameter is used for utilizing hot-spot avoidance with InfiniBand clusters. To leverage this functionality, the subnet should be configured with lmc greater than zero. Please refer to section 6.6 for detailed information.
This parameter enables the library to run in iWARP mode. The library has to be built using the flag -DRDMA_CM for using this feature.
Setting this parameter enables mvapich2 to use memory registration cache.
Setting this parameter enables mvapich2 to use memory registration cache. We recommend not to set this variable for the vapi device.
This parameter enables the use of RDMA CM for establishing the connections. The library has to be built using the flag -DRDMA_CM for using this feature.
Setting this parameter enables mvapich2 to use adaptive rdma fast path features for Gen2 devices and static rdma fast path features for uDAPL device.
Setting this parameter allows mvapich2 to use optimized one sided implementation based RDMA operations.
Setting this parameter enables mvapich2 to use ring based startup.
Use shared memory for intra-node communication.
This parameter can be used to turn off shared memory based MPI_Allreduce for Gen2 over IBA by setting this to 0.
This parameter can be used to turn off shared memory based MPI_Barrier for Gen2 over IBA by setting this to 0.
Use shared memory for collective communication. Set this to 0 for disabling shared memory collectives.
This parameter can be used to turn off shared memory based MPI_Reduce for Gen2 over IBA by setting this to 0.
Setting this parameter enables mvapich2 to use shared receive queue.
The number of vbufs in the initial pool. This pool is shared among all the connections.
The number of vbufs allocated each time when the global pool is running out in the initial pool. This is also shared among all the connections.
The size of each vbuf, the basic communication buffer of MVAPICH2.
This has no effect if macro _SMP_ is not defined. It defines the switch point from Eager protocol to Rendezvous protocol for intra-node communication. If macro _SMP_RNDV_ is defined, then for messages larger than SMP_EAGERSIZE, SMP Rendezvous protocol is used. Note that this variable should be set in KBytes.
This has no effect if macro _SMP_ is not defined. It defines the size of shared buffer between every two processes on the same node for transferring messages smaller than or equal to SMP_EAGERSIZE. Note that this variable should be set in KBytes.
This has no effect if macro _SMP_ is not defined. It defines the number of internal send buffers for sending intra-node messages larger than SMP_EAGERSIZE.
This has no effect if macro _SMP_ is not defined. It defines the packet size when sending intra-node messages larger than SMP_EAGERSIZE.