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Error running CosmoMC with Planck Likelihoods
 
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Carter Bartram



Joined: 05 May 2017
Posts: 3
Affiliation: Dartmouth College

PostPosted: May 05 2017  Reply with quote

Hello, I've installed the Planck data and linked everything correctly (at least I think so, as I used to get the "cannot stat file" error but no longer do). However, now when I try to run CosmoMC on test_planck.ini I get the following error:
Quote:
~/CosmoMC-Nov2016$ ./cosmomc test_planck.ini
Number of MPI processes: 1
file_root:test5
Random seeds: 15355, 7524 rand_inst: 1
compile with CLIK to use clik - see Makefile
MpiStop: 0
————————————————————————–
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 128.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
————————————————————————–

I've checked the Makefile, and the only reference to clik I could find was under camspec. I tried running make camspec, but the problem persists. What am I doing wrong?
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Jason Dossett



Joined: 19 Mar 2010
Posts: 97
Affiliation: The University of Texas at Dallas

PostPosted: May 05 2017  Reply with quote

Can you show us the output when you make, that is indicating that when you built, -DCLIK was not in the FFLAGS, so you may not have your environment set up correctly.

Did you do this:
Code:
source path_to_plc-2.0/bin/clik_profile.sh
echo -e "\nsource path_to_plc-2.0/bin/clik_profile.sh" >> ~/.bashrc


as described in the Planck Readme
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Carter Bartram



Joined: 05 May 2017
Posts: 3
Affiliation: Dartmouth College

PostPosted: May 06 2017  Reply with quote

This is the output from make camspec:

Code:
~/CosmoMC-Nov2016$ make camspec
cd ./source && make highL=../highL PLANCKLIKE=cliklike_CamSpec
make[1]: Entering directory '/home/ubuntu/CosmoMC-Nov2016/source'
mkdir -p ReleaseMPI
cd ../camb && \
make --file=Makefile_main libcamb OUTPUT_DIR=ReleaseMPI \
RECOMBINATION=recfast EQUATIONS=equations_ppf NONLINEAR=halofit_ppf
make[2]: Entering directory '/home/ubuntu/CosmoMC-Nov2016/camb'
mkdir -p ReleaseMPI
ar -r ReleaseMPI/libcamb_recfast.a ReleaseMPI/constants.o  ReleaseMPI/utils.o   ReleaseMPI/subroutines.o ReleaseMPI/inifile.o  ReleaseMPI/power_tilt.o  ReleaseMPI/recfast.o ReleaseMPI/reionization.o ReleaseMPI/modules.o ReleaseMPI/bessels.o ReleaseMPI/equations_ppf.o ReleaseMPI/halofit_ppf.o ReleaseMPI/lensing.o ReleaseMPI/SeparableBispectrum.o ReleaseMPI/cmbmain.o ReleaseMPI/camb.o
make[2]: Leaving directory '/home/ubuntu/CosmoMC-Nov2016/camb'
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c cliklike.f90 -o ReleaseMPI/cliklike.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c CMB.f90 -o ReleaseMPI/CMB.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c DataLikelihoods.f90 -o ReleaseMPI/DataLikelihoods.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c calclike.f90 -o ReleaseMPI/calclike.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c ImportanceSampling.f90 -o ReleaseMPI/ImportanceSampling.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c MCMC.f90 -o ReleaseMPI/MCMC.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c minimize.f90 -o ReleaseMPI/minimize.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c SampleCollector.f90 -o ReleaseMPI/SampleCollector.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c GeneralSetup.f90 -o ReleaseMPI/GeneralSetup.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c CalcLike_Cosmology.f90 -o ReleaseMPI/CalcLike_Cosmology.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c Calculator_CAMB.f90 -o ReleaseMPI/Calculator_CAMB.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c CosmologyConfig.f90 -o ReleaseMPI/CosmologyConfig.o
mpif90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/ -c driver.F90 -o ReleaseMPI/driver.o
mpif90 -o ../cosmomc ReleaseMPI/MiscUtils.o ReleaseMPI/ArrayUtils.o ReleaseMPI/StringUtils.o ReleaseMPI/MpiUtils.o ReleaseMPI/FileUtils.o ReleaseMPI/RandUtils.o ReleaseMPI/ObjectLists.o ReleaseMPI/Interpolation.o ReleaseMPI/IniObjects.o ReleaseMPI/ObjectParamNames.o ReleaseMPI/Matrix_utils_new.o  ReleaseMPI/settings.o ReleaseMPI/samples.o ReleaseMPI/IO.o ReleaseMPI/likelihood.o ReleaseMPI/GeneralTypes.o ReleaseMPI/BaseParameters.o ReleaseMPI/propose.o ReleaseMPI/ParamSet.o ReleaseMPI/PowellConstrainedMinimize.o ReleaseMPI/ImportanceSampling.o ReleaseMPI/MCMC.o ReleaseMPI/minimize.o ReleaseMPI/SampleCollector.o ReleaseMPI/GeneralSetup.o ReleaseMPI/CosmologyTypes.o ReleaseMPI/CosmoTheory.o ReleaseMPI/bbn.o ReleaseMPI/Calculator_Cosmology.o ReleaseMPI/CalcLike_Cosmology.o ReleaseMPI/Likelihood_Cosmology.o ReleaseMPI/Calculator_CAMB.o ReleaseMPI/CMB_BK_Planck.o ReleaseMPI/cliklike.o ReleaseMPI/mpk.o ReleaseMPI/wigglez.o ReleaseMPI/bao.o ReleaseMPI/supernovae_Union2.o ReleaseMPI/supernovae_SNLS.o ReleaseMPI/supernovae_JLA.o ReleaseMPI/szcounts.o ReleaseMPI/supernovae.o ReleaseMPI/HST.o  ReleaseMPI/CMB.o ReleaseMPI/CMBlikes.o ReleaseMPI/ElementAbundances.o ReleaseMPI/wl.o ReleaseMPI/CosmologyParameterizations.o ReleaseMPI/DataLikelihoods.o ReleaseMPI/calclike.o ReleaseMPI/CosmologyConfig.o ReleaseMPI/driver.o -L../camb/ReleaseMPI -lcamb_recfast -lblas -llapack   -L/home/ubuntu/Downloads/plc-2.0/lib -lclik_f90 -cpp -O3 -ffast-math -ffree-line-length-none -fopenmp -fmax-errors=4 -march=native -DMPI -DCLIK -I../camb/ReleaseMPI -I/home/ubuntu/Downloads/plc-2.0/include -JReleaseMPI -IReleaseMPI/
make[1]: Leaving directory '/home/ubuntu/CosmoMC-Nov2016/source'


I did the two lines from the readme again and double checked that my bashrc contains the path to clik_profile.sh.
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Antony Lewis



Joined: 23 Sep 2004
Posts: 1250
Affiliation: University of Sussex

PostPosted: May 08 2017  Reply with quote

You don't need to do "make camspec" (the option may be present in the Makefile as a relic of our Planck-internal version). Just use default make.
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Carter Bartram



Joined: 05 May 2017
Posts: 3
Affiliation: Dartmouth College

PostPosted: May 09 2017  Reply with quote

Well, I just reinstalled CosmoMC and everything now works fine. Thanks for your help.
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