CosmoCoffee Forum Index CosmoCoffee

 
 FAQFAQ   SearchSearch  MemberlistSmartFeed   MemberlistMemberlist    RegisterRegister 
   ProfileProfile   Log inLog in 
Arxiv New Filter | Bookmarks & clubs | Arxiv ref/author:

Errors when making cosmomc
 
Post new topic   Reply to topic    CosmoCoffee Forum Index -> Computers and software
View previous topic :: View next topic  
Author Message
Albin Nilsson



Joined: 05 Oct 2016
Posts: 13
Affiliation: NCBJ, Warsaw
PostPosted: December 20 2016  Reply with quote
I'm installing cosmomc on our cluster, and here's an error I have been unable to solve.
I can install the Planck PLC with no trouble, but when I try to make cosmomc it throws me the following (I am using ifort and mpif90 with the ifort flag).
I tried a global search for the missing files in order to link them in manually, but cannot find them anywhere.
Any ideas are welcome, thanks in advance!

Code:

mpif90 -f90=ifort -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    -L/mnt/opt/groups/app-qcosmo/cosmomc/planckdata_and_plc/plc-2.0/lib -lclik_f90 -mkl -O3 -no-prec-div -fpp -openmp -xHost -DMPI -DCLIK -I../camb/ReleaseMPI -I/mnt/opt/groups/app-qcosmo/cosmomc/planckdata_and_plc/plc-2.0/include -module ReleaseMPI -IReleaseMPI/
ld: warning: libibmad.so.5, needed by /mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpichf90.so, not found (try using -rpath or -rpath-link)
ld: warning: librdmacm.so.1, needed by /mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpichf90.so, not found (try using -rpath or -rpath-link)
ld: warning: libibumad.so.3, needed by /mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpichf90.so, not found (try using -rpath or -rpath-link)
ld: warning: libibverbs.so.1, needed by /mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpichf90.so, not found (try using -rpath or -rpath-link)
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `mad_get_field@IBMAD_1.3'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `ibv_modify_qp@IBVERBS_1.1'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `umad_release_ca@IBUMAD_1.0'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `umad_register@IBUMAD_1.0'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `rdma_disconnect@RDMACM_1.0'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `ibv_create_qp@IBVERBS_1.1'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `ibv_destroy_qp@IBVERBS_1.1'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `umad_open_port@IBUMAD_1.0'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `ibv_destroy_ah@IBVERBS_1.1'
/mnt/opt/tools/slc6/mvapich2/1.9a/lib/libmpich.so: undefined reference to `ibv_reg_xrc_rcv_qp@IBVERBS_1.1'
Back to top
View user's profile  
Jason Dossett



Joined: 19 Mar 2010
Posts: 97
Affiliation: The University of Texas at Dallas
PostPosted: December 22 2016  Reply with quote
Just out of curiousity, it appears you have intel compilers installed. Do you know if you have the cluster version of the compilers? If so, you could try mpiifort and build with intel's mpi interface.

It looks like the version of mpich which you are using was compiled with a need for some infiniband related libraries that for some reason your system is now unable to find.

You can try running the following command and see if you get anything. Since I dont know what system you are on I am not positive it will work, but you can give it a try.

Code:
ldconfig -p | grep libibmad
Back to top
View user's profile [ Hidden ] Visit poster's website
Display posts from previous:   
Post new topic   Reply to topic    CosmoCoffee Forum Index -> Computers and software All times are GMT + 5 Hours
Page 1 of 1

 
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum


Powered by phpBB © 2001, 2005 phpBB Group. Sponsored by WordWeb online dictionary and dictionary software.