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Compiling Open Tool for Parameter Optimization (otpo)

Taken from Open Tool for Parameter Optimization (otpo) Documentation

OTPO (Open Tool for Parameter Optimizations) is an Open MPI specific tool that is meant to explore the MCA parameter space. In Open MPI, the user can specify at runtime many values for MCA parameters, try e.g. (ompi_info –param all all). Alternatively, to focus on a single aspect of parameters, e.g. the parameters of the OpenIB BTL (ompi_info –param btl openib).

OTPO is a tool that takes in a list of any MCA parameters, with a user specified range of values for those parameters, and for every combination of the MCA parameter values, OTPO executes an MPI job, measuring execution time (the only measurement available right now), bandwidth, etc.. The tests used for the measurements are modular. Right now, OTPO supports

Netpipe
Skampi
NAS Parallel Benchmarks

OTPO outputs a list of the best parameter combinations for a certain test.

The main purpose of OTPO is to explore the effect of the MCA parameters on different machines with different architectures and configurations, and explore the dependencies between the MCA parameters themselves. OTPO is meant to run on the head node of a cluster, and it forks MPI jobs after exporting the current combination of MCA parameters on the nodes.

OTPO is built on top of ADCL (Abstract Data and Communication Library). ADCL is an application level communication library aiming at providing the highest possible performance for application level communication operations in a given execution environment. OTPO uses ADCL to provide the runtime selection logic and choosing the best combination of parameters.

A. Compiling OTPO

Step 1: Make sure your PATH and LD_LIBRARY_PATH has the necessary pathing for the OpenMPI and Compilers

In your .bashrc, it should look something like

export PATH=$PATH:/usr/local/intel/composerxe/bin:/usr/local/openmpi-1.6.5-intel-v12.1.5/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1/lib:/usr/local/intel/composerxe/lib/intel64:/usr/local/intel/composerxe/mkl/lib/intel64:/usr/local/openmpi-1.6.5-intel-v12.1.5/lib

Step 2: Download and compile ADCL within OTPO

# wget http://www.open-mpi.org/software/otpo/v1.0/downloads/otpo-1.0.tar.gz
# tar -zxvf otpo-1.0.tar.gz
# cd otpo
# cd ADCL
# ./configure --prefix=/usr/local/ADCL
# make
# make install
# cp /root/otpo/ADCL/include/*.h /usr/local/ADCL

After the compilation, you should see libadcl.a inside the lib folder of ADCL. Remember to copy the ADCL headers to the /usr/local/ADCL/include

Step 3: Compile OTPO

# ./autogen.sh
# ./configure --prefix=/usr/local/otpo-1.0 --with-adcl-dir=/usr/local/ADCL
# make
# make install
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Compiling VASP 5.3.3 with OpenMPI 1.6.5 and Intel 12.1.5

Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

To compile VASP, I will be using the following

  1. Intel Compiler XE 12.1.5
  2. OpenMPI 1.6.5
  3. Maths Kernel Library (MKL)
  4. CentOS 6.3 / RH 6.3

A. Prerequisites

Step 1: Install and Compile Intel XE Compilers 12.1.5 and OpenMPI 1.6.5

  1. Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentO 6

Step 2: Intel MKL FFTW wrappers

  1. Compile and Build FFTW3 wrapper routines on MKL implementation of FFT

B. Compiling VASP Libraries

Assuming you have unpacked the VASP files. Here is may make file

.SUFFIXES: .inc .f .F
#-----------------------------------------------------------------------
# Makefile for LINUX NAG f90
#-----------------------------------------------------------------------
# fortran compiler
FC=ifort

# C-preprocessor
#CPP     = /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C $*.F >$*.f
CPP      = gcc -E -P -C -DLONGCHAR $*.F >$*.f

CFLAGS = -O
FFLAGS = -Os -FI
FREE   = -FR

DOBJ =  preclib.o timing_.o derrf_.o dclock_.o  diolib.o dlexlib.o drdatab.o

#-----------------------------------------------------------------------
# general rules
#-----------------------------------------------------------------------

libdmy.a: $(DOBJ) linpack_double.o
-rm libdmy.a
ar vq libdmy.a $(DOBJ)

linpack_double.o: linpack_double.f
$(FC) $(FFLAGS) $(NOFREE) -c linpack_double.f

# files which do not require autodouble
lapack_double.o: lapack_double.f
$(FC) $(FFLAGS) $(NOFREE) -c lapack_double.f
lapack_single.o: lapack_single.f
$(FC) $(FFLAGS) $(NOFREE) -c lapack_single.f
#lapack_cray.o: lapack_cray.f
#       $(FC) $(FFLAGS) $(NOFREE) -c lapack_cray.f

.c.o:
$(CC) $(CFLAGS) -c $*.c
.F.o:
$(CPP)
$(FC) $(FFLAGS) $(FREE) $(INCS) -c $*.f
.F.f:
$(CPP)
.f.o:
$(FC) $(FFLAGS) $(FREE) $(INCS) -c $*.f

C. Compiling VASP

1. Copy the Makefile from makefile.linux_ifc_P4 in the vasp software.

# cp makefile.linux_ifc_P4 Makefile

2. Edit the Makefile

FC (~ line 62)

#-----------------------------------------------------------------------
# fortran compiler and linker
#-----------------------------------------------------------------------
FC=mpif90
# fortran linker
FCL=$(FC) -mkl

FFLAGS (~line 108)

#-----------------------------------------------------------------------
# general fortran flags  (there must a trailing blank on this line)
# byterecl is strictly required for ifc, since otherwise
# the WAVECAR file becomes huge
#-----------------------------------------------------------------------

FFLAGS =  -FR -names lowercase -assume byterecl

BLAS (~ line 149)

# BLAS
# setting -DRPROMU_DGEMV  -DRACCMU_DGEMV in the CPP lines usually speeds up program execution
# BLAS= -Wl,--start-group $(MKL_PATH)/libmkl_intel_lp64.a $(MKL_PATH)/libmkl_intel_thread.a $(MKL_PATH)/libmkl_core.a -Wl,--end-group -lguide
# faster linking and available from at least version 11
BLAS= -mkl=sequential

LAPACK (~ line 158)

# LAPACK from mkl, usually faster and contains scaLAPACK as well
#LAPACK= $(MKL_PATH)/libmkl_intel_lp64.a
LAPACK =

CPP ( ~ line 223)

#-----------------------------------------------------------------------
CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \
-DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf \
-DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK \
-DRPROMU_DGEMV -DRACCMU_DGEMV

SCALAPACK (~ line 233)

#-----------------------------------------------------------------------
# location of SCALAPACK
# if you do not use SCALAPACK simply leave this section commented out
#-----------------------------------------------------------------------

# usually simplest link in mkl scaLAPACK
BLACS= -lmkl_blacs_openmpi_lp64
SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)

LIBRARIES (~line 238)

#-----------------------------------------------------------------------
# libraries
#-----------------------------------------------------------------------

LIB = -L../vasp.5.lib -ldmy \
../vasp.5.lib/linpack_double.o \
$(SCA) $(LAPACK) $(BLAS)

Parallel FFT (~ line 246)

#-----------------------------------------------------------------------
# parallel FFT
#-----------------------------------------------------------------------

# FFT: fftmpi.o with fft3dlib of Juergen Furthmueller
FFT3D = fftmpi.o fftmpi_map.o fft3dfurth.o fft3dlib.o

References:

  1. Building VASP* with Intel® MKL and Intel® Compilers

    2. (Intel Developer Zone)

  2. How to Compile VASP on NSC’s Triolith
  3. Installing VASP
  4. How to build VASP-4.6.36 and VASP-5.2.8 on Intel Westmere with Infiniband network
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Compiling GCC 4.7.2 on CentOS 5

Step 1: Download the following prerequistics applications libraries from ftp://gcc.gnu.org/pub/gcc/infrastructure/

  1. gmp-4.3.2.tar.bz2
  2. mpfr-2.4.2.tar.bz2
  3. mpc-0.8.1.tar.gz

1. Install gmp-4.3.2

# bunzip2 gmp-4.3.2.tar.bz2
# tar -zxvf gmp-4.3.2.tar
# cd gmp-4.3.2
# ./configure --prefix=/usr/local/gmp-4.3.2
# make
# make install

2. Install mpfr-2.4.2 (requires gmp-4.3.2 as prerequisites)

# bunzip2 mpfr-2.4.2.tar.bz2
# tar -zxvf mpfr-2.4.2.tar
# cd mpfr-2.4.2
# ./configure --prefix=/usr/local/mpfr-2.4.2 --with-gmp=/usr/local/gmp-4.3.2/
# make
# make install

3. Install mpc-0.8.1 (requires gmp-4.3.2 and mpfr-2.4.2 as prerequisites ) 

# tar -zxvf mpc-0.8.1.tar.gz
# cd mpc-0.8.1
#./configure --prefix=/usr/local/mpc-0.8.1/ --with-gmp=/usr/local/gmp-4.3.2/ --with-mpfr=/usr/local/mpfr-2.4.2
# make
# make install

4. Update your LD_LIBRARY_PATH at your ~/.bashrc

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1:/usr/local/mpfr-2.4.2/lib:/usr/local/gmp-4.3.2/lib

5. Install the glibc-devel.i686. For more information, do look at Error when compiling GCC 4.8.1 (linuxtoolkit.blogspot.com)

6. Finally install GNU CC 4.7.2

# tar -zxvf  gcc-4.7.2.tar.gz
# cd gcc-4.7.2
# mkdir build-gcc
# cd build-gcc
# ../configure --prefix=/usr/local/gcc-4.7.2 \ 
--with-mpfr=/usr/local/mpfr-2.4.2 \ 
--with-mpc=/usr/local/mpc-0.8.1 \
--with-gmp=/usr/local/gmp-4.3.2 \
--with-mpfr-include=/usr/local/mpfr-2.4.2/include \
--with-mpc-include=/usr/local/mpc-0.8.1/include
# make all-gcc
# make install-gcc
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Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentOS 6

Step 1: Download the OpenMPI Software from http://www.open-mpi.org/ . The current stable version at point of writing is OpenMPI 1.6.5

Step 2: Download and Install the Intel Compilers from Intel Website. More information can be taken from Free Non-Commercial Intel Compiler Download

Step 3: Add the Intel Directory Binary Path to the Bash Startup

At my ~/.bash_profile directory, I've added
source /usr/local/intel/composerxe/bin/compilervars.sh intel64
export PATH=$PATH:/usr/local/intel/composerxe/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/RH6_apps/intel/composerxe/lib/intel64:/usr/local/intel/composerxe/mkl/lib/intel64

At command prompt

# source .bashrc

Step 4: Configuration Information

# gunzip -c openmpi-1.6.5.tar.gz tar xf -
# cd openmpi-1.6.5
# /configure --prefix=/usr/local/openmpi-1.6.5-intel-v12.1.5 CC=icc CXX=icpc F77=ifort FC=ifort --with-devel-headers --enable-binaries
# make all install

You will need to include –devel-headers –enable-binaries” or you will face the error Cannot open OpenMPI Configuration mpif90-wrapper-data.txt

Step 5: Test the configuration

$ mpicc -v
cc version 12.1.5 (gcc version 4.4.6 compatibility)
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Building OpenMPI Libraries for 64-bit integers

There is an excellent article on how to build OpenMPI Libraries for 64-bit integers. For more detailed information, do look at How to build MPI libraries for 64-bit integers

The information on this website is taken from the above site.

Step 1: Check the integer size. Do the following. If the output is as below, you have to compile OpenMPI with 64 bits.

# ompi_info -a | grep 'Fort integer size'
Fort integer size: 4

Intel Compilers Step 2a: To compile OpenMPI with Intel Compilers and with 64-bits integers, do the following:

# ./configure --prefix=/usr/local/openmpi CXX=icpc CC=icc 
F77=ifort FC=ifort FFLAGS=-i8 FCFLAGS=-i8
# make -j 8
# make install

* GNU Compilers

Step 2b: To compile OpenMPI with GNU Compilers and with 64-bits, do the followings:

# ./configure --prefix=/usr/local/openmpi CXX=g++ CC=gcc F77=gfortran FC=gfortran \
FFLAGS="-m64 -fdefault-integer-8"       \
CFLAGS="-m64 -fdefault-integer-8"      \
CFLAGS=-m64                             \
CXXFLAGS=-m64
# make -j 8
# make install

Step 3: Update your PATH and LD_LIBRARY_PATH in your .bashrc

export $PATH=/usr/local/openmpi/bin:$PATH 
export $LD_LIBRARY_PATH=/usr/local/openmpi/lib:$LD_LIBRARY_PATH

Verify that the installation is correct

# ompi_info -a | grep 'Fort integer size' 
Fort integer size: 8
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Registering sufficent memory for OpenIB when using Mellanox HCA

If you encountered errors like “error registering openib memory” similar to what is written below. You may want to take a look at the OpenMPI FAQ – I’m getting errors about “error registering openib memory”; what do I do? .

WARNING: It appears that your OpenFabrics subsystem is configured to only
allow registering part of your physical memory.  This can cause MPI jobs to
run with erratic performance, hang, and/or crash.

This may be caused by your OpenFabrics vendor limiting the amount of
physical memory that can be registered.  You should investigate the
relevant Linux kernel module parameters that control how much physical
memory can be registered, and increase them to allow registering all
physical memory on your machine.

See this Open MPI FAQ item for more information on these Linux kernel module
parameters:

    http://www.open-mpi.org/faq/?category=openfabrics#ib-locked-pages

  Local host:              node02
  Registerable memory:     32768 MiB
  Total memory:            65476 MiB

Your MPI job will continue, but may be behave poorly and/or hang.

The explanation solution can be found at How to increase MTT Size in Mellanox HCA.

In summary, the error occurred when applications which consumed a large amount of memory, application might fail when not enough memory can be registered with RDMA. There is a need to increase MTT size. But increasing MTT size hasve the downside of increasing the number of “cache misses” and increases latency.

1. To check your value of log_num_mtt

# cat /sys/module/mlx4_core/parameters/log_num_mtt

2. To check your value of log_mtts_per_seg

# cat /sys/module/mlx4_core/parameters/log_mtts_per_seg

There are 2 parameters that affect registered memory. This can be taken from http://www.open-mpi.org/faq/?category=openfabrics#ib-low-reg-mem

With Mellanox hardware, two parameters are provided to control the size of this table:

  • log_num_mtt (on some older Mellanox hardware, the parameter may benum_mtt, not log_num_mtt): number of memory translation tables
  • log_mtts_per_seg:

The amount of memory that can be registered is calculated using this formula:

In newer hardware:
    max_reg_mem = (2^log_num_mtt) * (2^log_mtts_per_seg) * PAGE_SIZE

In older hardware: 
    max_reg_mem = num_mtt * (2^log_mtts_per_seg) * PAGE_SIZE

For example if your server’s Physical Memory is 64GB RAM. You will need to registered 2 times the Memory (2x64GB=128GB) for the max_reg_mem. You will also need to get the PAGE_SIZE (See Virtual Memory PAGESIZE on CentOS)

max_reg_mem = (2^ log_num_mtt) * (2^3) * (4 kB)
128GB = (2^ log_num_mtt) * (2^3) * (4 kB)
2^37 = (2^ log_num_mtt) * (2^3) * (2^12)
2^22 = (2^ log_num_mtt)
22 = log_num_mtt

The setting is found in /etc/modprobe.d/mlx4_mtt.conf for every nodes.

References:

  1. OpenMPI FAQ – 15. I’m getting errors about “error registering openib memory”; what do I do?
  2. How to increase MTT Size in Mellanox HCA
  3. OpenMPI FAQ – 18. Open MPI is warning me about limited registered memory; what does this mean?
  4. Virtual Memory PAGESIZE on CentOS
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Tracking Batch Jobs at Platform LSF

The content article is taken from http://users.cs.fiu.edu/~tho01/psg/3rdParty/lsf4_userGuide/07-tracking.html

1. Displaying All Job Status

# bjobs -u all

2. Report Reasons why a job is pending

# bjobs -p

3. Report Pending Reasons with host names for each conditions

# bjobs -lp

4. Detailed Report on a specific jobs

# bjobs -l 6653

5. Reasons why the job is suspended

# bjobs -s

6. Displaying Job History

# bpeek 12345

7. Killing Jobs

# bkill 12345

8. Stop the Job

# bstop 12345

9 Resume the job

# bresume 12345