Matrix Product State (MPS) Simulations / Tickets / #32 How install in CentOS 6?

Daniel Jaschke - 2019-07-01

Hi Suman,

cluster are always difficult to give advice. I have two things in mind

1) If it is a university cluster, they might have some pre-installed
modules including LAPACK and BLAS, which you can load and link (sometimes
even without specifying the whole path.). The time figuring out how to do
this is usually a good investment, especially if you can use intel
compilers then. You can compile it yourself, but user rights are usually
limited. But I am glad you were able to do it.
2) You seem to have trouble with Arpack. Arpack is only used for iMPS
(infinite MPS) and not the same as LAPACK/BLAS. If you are using only the
finite-size systems right now and have a newer version of OSMPS, you can
compile without Arpack. I believe it should be sufficient to pass
--ARPACK_FLAG='' to overwrite the default when calling BuildOSMPS.py. Matt
has changed some interface for compiling, so I cannot tell right now. But
if you still have trouble there after a try, let me know and we will look
into it.

That is the quick overview, we can go into more details if necessary.

Best regards,

Daniel

On Mon, Jul 1, 2019 at 7:31 AM Suman Mondal sumanf40@users.sourceforge.net
wrote:

[tickets:#32] https://sourceforge.net/p/openmps/tickets/32/ How
install in CentOS 6?*

Status: open
Milestone: 1.0
Created: Mon Jul 01, 2019 05:31 AM UTC by Suman Mondal
Last Updated: Mon Jul 01, 2019 05:31 AM UTC
Owner: nobody

Hi,
I want to install it on a high-performance computer cluster running on
CentOS 6. When I am trying to install it using 'python BuildOSMPS.py' is
raising error which is quoted below.

"
make MPSMain > make.log 2>&1
python deref.py make.log
head -n 40 make.log
gfortran
cd /home/suman.m/openMPS/MPSFortLib/Mods/; python TemplateGenerator.py
/home/suman.m/openMPS/MPSFortLib/Mods/BasicOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/IOOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/LinearAlgebra.o
/home/suman.m/openMPS/MPSFortLib/Mods/ExpokitOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/Tensors.o
/home/suman.m/openMPS/MPSFortLib/Mods/qTensors.o
/home/suman.m/openMPS/MPSFortLib/Mods/ContractionOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/DecompositionOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/MPOOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/MPSOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/MPDOOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/LPTNOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/LanczosOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/Convergence.o
/home/suman.m/openMPS/MPSFortLib/Mods/ObsOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/VariationalOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/iMPSOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/KrylovOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/TDVPOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/TEBDOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/ZaletelOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/TimeEvolutionOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/PyInterface.o --mpi=gfortran --dbg=F
--imps=T --macacc=F
cd /home/suman.m/openMPS/MPSFortLib/Mods/; make all
make[1]: Entering directory /home/suman.m/openMPS/MPSFortLib/Mods'
make[1]: Nothing to be done forall'.
make[1]: Leaving directory `/home/suman.m/openMPS/MPSFortLib/Mods'
gfortran -O3 -c MPSMain.f90 -I/home/suman.m/openMPS/MPSFortLib/Mods/
gfortran -O3 -o Execute_MPSMain MPSMain.o
/home/suman.m/openMPS/MPSFortLib/Mods/BasicOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/IOOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/LinearAlgebra.o
/home/suman.m/openMPS/MPSFortLib/Mods/ExpokitOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/Tensors.o
/home/suman.m/openMPS/MPSFortLib/Mods/qTensors.o
/home/suman.m/openMPS/MPSFortLib/Mods/ContractionOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/DecompositionOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/MPOOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/MPSOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/MPDOOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/LPTNOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/LanczosOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/Convergence.o
/home/suman.m/openMPS/MPSFortLib/Mods/ObsOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/VariationalOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/iMPSOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/KrylovOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/TDVPOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/TEBDOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/ZaletelOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/TimeEvolutionOps.o
/home/suman.m/openMPS/MPSFortLib/Mods/PyInterface.o -larpack -llapack
-lblas -I/home/suman.m/openMPS/MPSFortLib/Mods/
/usr/bin/ld: cannot find -larpack
collect2: error: ld returned 1 exit status
make: *** [MPSMain] Error 1
rm MPSMain.o
mv MPSFortLib/make.log .
"

Before installing OSMPS I have installed these packages:
blas-3.2.1-5.el6.x86_64.rpm
blas-devel-3.2.1-5.el6.x86_64.rpm
lapack-3.2.1-5.el6.x86_64.rpm
lapack-devel-3.2.1-5.el6.x86_64.rpm.
Could you please help me to install it on CentOS 6.

Thanks and regards,
Suman

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Matthew Jones - 2019-07-01

It looks like the linker can't find ARPACK. Can you confirm it's installed on the system?

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- Suman Mondal - 2019-07-03
  
  I am not able to find LAPACK package for CentOS
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Matthew Jones - 2019-07-01

Also, as Daniel pointed out, to prevent the build script from linking ARPACK, simply pass this to the command line in place of command documented on our Wiki:

python BuildOSMPS.py --prefix=$CONDA_PREFIX/bin \ --option=FC:x86_64-conda_cos6-linux-gnu-gfortran \ --option=INCFLAGS:-I$CONDA_PREFIX/include \ --option=LIBFLAGS:-L$CONDA_PREFIX/lib --option=ARPACK_FLAG:''

EDIT: If you're not averse to Anaconda package management, the above Wiki will instruct you on grabbing all necessary dependencies and building from source within a virtual environment. I've also added some notes below.

NOTE: You may change the paths in prefix, FC, INCFLAGS, and LIBFLAGS to suit your system's setup.

prefix is a keyword that tells the build script where to install the executable. /usr/local/bin is a common choice. You can also place it in a custom location, but it should be discoverable in your PATH variable so that Python picks it up when running simulations, on import, etc.

FC should point to your Fortran compiler.

INCFLAGS should contain all include path directories.

LIBFLAGS should contain all library path directories

ARPACK_FLAG is an override for linking ARPACK. Setting it to null ('') will prevent the compiler from linking ARPACK to the object binaries.

Last edit: Matthew Jones 2019-07-02
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Suman Mondal - 2019-07-03

Hello!
I have tried to install it by:
python BuildOSMPS.py --option=ARPACK_FLAG:''

It is still raising the following message:
make MPSMain > make.log 2>&1
python deref.py make.log
head -n 40 make.log
gfortran
cd /home/suman.m/openMPS/MPSFortLib/Mods/; python TemplateGenerator.py /home/suman.m/openMPS/MPSFortLib/Mods/BasicOps.o /home/suman.m/openMPS/MPSFortLib/Mods/IOOps.o /home/suman.m/openMPS/MPSFortLib/Mods/LinearAlgebra.o /home/suman.m/openMPS/MPSFortLib/Mods/ExpokitOps.o /home/suman.m/openMPS/MPSFortLib/Mods/Tensors.o /home/suman.m/openMPS/MPSFortLib/Mods/qTensors.o /home/suman.m/openMPS/MPSFortLib/Mods/ContractionOps.o /home/suman.m/openMPS/MPSFortLib/Mods/DecompositionOps.o /home/suman.m/openMPS/MPSFortLib/Mods/MPOOps.o /home/suman.m/openMPS/MPSFortLib/Mods/MPSOps.o /home/suman.m/openMPS/MPSFortLib/Mods/MPDOOps.o /home/suman.m/openMPS/MPSFortLib/Mods/LPTNOps.o /home/suman.m/openMPS/MPSFortLib/Mods/LanczosOps.o /home/suman.m/openMPS/MPSFortLib/Mods/Convergence.o /home/suman.m/openMPS/MPSFortLib/Mods/ObsOps.o /home/suman.m/openMPS/MPSFortLib/Mods/VariationalOps.o /home/suman.m/openMPS/MPSFortLib/Mods/KrylovOps.o /home/suman.m/openMPS/MPSFortLib/Mods/TDVPOps.o /home/suman.m/openMPS/MPSFortLib/Mods/TEBDOps.o /home/suman.m/openMPS/MPSFortLib/Mods/ZaletelOps.o /home/suman.m/openMPS/MPSFortLib/Mods/TimeEvolutionOps.o /home/suman.m/openMPS/MPSFortLib/Mods/PyInterface.o --mpi=gfortran --dbg=F --imps=F --macacc=F
cd /home/suman.m/openMPS/MPSFortLib/Mods/; make all
make[1]: Entering directory /home/suman.m/openMPS/MPSFortLib/Mods' make[1]: Nothing to be done forall'.
make[1]: Leaving directory /home/suman.m/openMPS/MPSFortLib/Mods' gfortran -O3 -c MPSMain.f90 -I/home/suman.m/openMPS/MPSFortLib/Mods/ gfortran -O3 -o Execute_MPSMain MPSMain.o /home/suman.m/openMPS/MPSFortLib/Mods/BasicOps.o /home/suman.m/openMPS/MPSFortLib/Mods/IOOps.o /home/suman.m/openMPS/MPSFortLib/Mods/LinearAlgebra.o /home/suman.m/openMPS/MPSFortLib/Mods/ExpokitOps.o /home/suman.m/openMPS/MPSFortLib/Mods/Tensors.o /home/suman.m/openMPS/MPSFortLib/Mods/qTensors.o /home/suman.m/openMPS/MPSFortLib/Mods/ContractionOps.o /home/suman.m/openMPS/MPSFortLib/Mods/DecompositionOps.o /home/suman.m/openMPS/MPSFortLib/Mods/MPOOps.o /home/suman.m/openMPS/MPSFortLib/Mods/MPSOps.o /home/suman.m/openMPS/MPSFortLib/Mods/MPDOOps.o /home/suman.m/openMPS/MPSFortLib/Mods/LPTNOps.o /home/suman.m/openMPS/MPSFortLib/Mods/LanczosOps.o /home/suman.m/openMPS/MPSFortLib/Mods/Convergence.o /home/suman.m/openMPS/MPSFortLib/Mods/ObsOps.o /home/suman.m/openMPS/MPSFortLib/Mods/VariationalOps.o /home/suman.m/openMPS/MPSFortLib/Mods/KrylovOps.o /home/suman.m/openMPS/MPSFortLib/Mods/TDVPOps.o /home/suman.m/openMPS/MPSFortLib/Mods/TEBDOps.o /home/suman.m/openMPS/MPSFortLib/Mods/ZaletelOps.o /home/suman.m/openMPS/MPSFortLib/Mods/TimeEvolutionOps.o /home/suman.m/openMPS/MPSFortLib/Mods/PyInterface.o -llapack -lblas -I/home/suman.m/openMPS/MPSFortLib/Mods/ /home/suman.m/openMPS/MPSFortLib/Mods/PyInterface.o: In functionpyinterface_MOD_runmps':
PyInterface.f90:(.text+0x43600): undefined reference to __impsops_MOD_infinitemps_mps' PyInterface.f90:(.text+0x4433b): undefined reference toimpsops_MOD_infinitemps_mpsc'
/cm/shared/apps/lapack/open64/64/3.6.0/liblapack.so(dgesvd.o): In function dgesvd_': /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dgesvd.f:313: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dgesvd.f:313: undefined reference to s_copy' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dgesvd.f:474: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dgesvd.f:474: undefined reference to s_copy' /cm/shared/apps/lapack/open64/64/3.6.0/liblapack.so(dhseqr.o): In functiondhseqr_':
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dhseqr.f:453: undefined reference to s_cat' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dhseqr.f:453: undefined reference tos_copy'
/cm/shared/apps/lapack/open64/64/3.6.0/liblapack.so(dlange.o): In function dlange_': /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dlange.f:165: undefined reference tos_cmp'
/cm/shared/apps/lapack/open64/64/3.6.0/liblapack.so(dormbr.o): In function dormbr_': /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:273: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:273: undefined reference to s_copy' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:281: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:281: undefined reference to s_copy' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:276: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:276: undefined reference to s_copy' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:284: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormbr.f:284: undefined reference to s_copy' /cm/shared/apps/lapack/open64/64/3.6.0/liblapack.so(dormhr.o): In functiondormhr_':
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormhr.f:252: undefined reference to s_cat' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormhr.f:252: undefined reference tos_copy'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormhr.f:254: undefined reference to s_cat' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormhr.f:254: undefined reference tos_copy'
/cm/shared/apps/lapack/open64/64/3.6.0/liblapack.so(dormlq.o): In function dormlq_': /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormlq.f:247: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormlq.f:247: undefined reference to s_copy' /usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormlq.f:272: undefined reference tos_cat'
/usr/src/redhat/BUILD/lapack-3.6.0/SRC/dormlq.f:272: undefined reference to `s_copy'
mv MPSFortLib/make.log .

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Suman Mondal - 2019-07-03

Hello,
I have tried to install it with
python BuildOSMPS.py --option=ARPACK_FLAG:''

The raised output message is attached in the attachment.

Regards,
Suman

message.txt

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- Matthew Jones - 2019-07-08
  
  It looks like it didn't like passing a null character. Passing --option=ARPACK_FLAG:' ' gets it past these copy errors.
  
  Unfortunately, it looks like there's a new error from trying to compile iMPS modules:
  
  iMPSOps.f90:(.text+0x1757c): undefined reference to `zneupd_'
  
  I'm not aware of a clean way not to compile the iMPS targets to avoid the ARPACK dependency. I'd have to make some changes to the build scripts to facilitate avoiding these targets.
  
  Is there a reason you can't install ARPACK? It would be good to know, and would help us prioritize feature modularity within our lirbary.
  
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Suman Mondal - 2019-07-11

Hello Matthew,
Thank you for replying. I was searching for the ARPACK packege for CentOS 6 but there is no ARPACK packege in the website.

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- Matthew Jones - 2019-07-11
  
  So, my CentOS 6 is a touch rusty, but the ARPACK binaries are available under the EPEL (Extra Pacakges for Enterprise Linux) repo. You can verify that EPEL is active by running
  
  yum repolist
  
  If you don't see an item that looks like epel: ..., then you can add it with
  
  wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-6.noarch.rpm && \ yum install ./epel-release-latest-*.noarch.rpm
  
  After this, rerun yum repolist to confirm that you see an entry for epel. Once enabled, you can install ARPACK via the following command:
  
  yum check-update && \ yum install arpack
  
  Some references:
  ARPACK on CentOS6
  Recent article on enabling EPEL on CentOS6
  
  Note: there is a quick how-to instruction set for installing the EPEL release on CentOS6. This may not grab the latest release (I didn't test this). The article on enabling EPEL does grab the latest EPEL release from the Fedora Project.
  
  Last edit: Matthew Jones 2019-07-11
  
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Daniel Jaschke - 2019-07-11

Hi everyone,

my personal approach would be not to install Arpack if you do not run infinite-size MPS (iMPS). I have attached you an older version of the BuildOSMPS.py script, which is named build.py to avoid name conflicts. Starting around line 96, it has pre-defined sets of build options, which once worked on one of our architectures. For example you can hijack the unix from line 110 and replace the ARPACK entry with an empty string. Then, you should be able to call

python build.py --prefix='.' --os=unix --clean

Prefix sets the installation path, where dot is the current folder. The os optional loads one of the predefined settings, which have been mostly used for different operating systems. The clean option is only necessary for the first compilation to get rid of whatever files are still around from the most recent compiling efforts. You might have to adapt LAPACK flags, but you figured this out once already.

Best regards,

Daniel

build.py

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How install in CentOS 6?

Numerical routines for variational matrix product state simulations.

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#32 How install in CentOS 6?

Could you please help me to install it on CentOS 6.

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