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Re: [igraph] Compiling igraph with the Intel compilers

From: Gábor Csárdi
Subject: Re: [igraph] Compiling igraph with the Intel compilers
Date: Wed, 31 Oct 2012 10:47:04 -0400


the problem is that you added the function to all these files, and
then there will be multiple copies of it at linking time. Take a look
at this patch:

If you want to build the R package, then you only need to update
igraph_types.h and other.c, exactly in the way shown in the patch.
(And undo your other updates.)

Unfortunately I cannot try this with the intel compilers now, but if
you experience more problems, please let me know.


On Wed, Oct 31, 2012 at 9:46 AM, Malcolm Tobias <address@hidden> wrote:
> I'm attempting to install igraph 0.6-3 using the Intel 12.1 compilers.
> I've encountered this error:
> foreign-gml-parser.c(971): error: expression must be a pointer to a complete
> object type
> which appears to be a known bug:
> http://lists.nongnu.org/archive/html/igraph-help/2012-06/msg00048.html
> and the fix is to add:
> char* stpcpy(char* s1, const char* s2) {
> char* result = strcpy(s1, s2);
> return result + strlen(s1);
> }
> This resolves the error message, but then I found I needed to apply it to:
> foreign-lgl-parser.c
> foreign-ncol-parser.c
> foreign-pajek-parser.c
> While this fixes the compilation of the individual files, I'm getting a
> link-time error:
> icpc -shared -L/export/intel/Compiler/12.1/lib/intel64/ -o igraph.so
> DensityGrid.o DensityGrid_3d.o NetDataTypes.o NetRoutines.o adjlist.o
> amd_1.o amd_2.o amd_aat.o amd_control.o amd_defaults.o amd_dump.o amd_info.o
> amd_order.o amd_post_tree.o amd_postorder.o amd_preprocess.o amd_valid.o
> arpack.o array.o atlas.o attributes.o basic_query.o bfgs.o bigint.o bignum.o
> bipartite.o blas.o bliss.o bliss_eqrefhash.o bliss_graph.o bliss_heap.o
> bliss_orbit.o bliss_partition.o bliss_timer.o bliss_utils.o cattributes.o
> centrality.o cliques.o clustertool.o cocitation.o cohesive_blocks.o colamd.o
> community.o complex.o components.o conversion.o cores.o cs_add.o cs_amd.o
> cs_chol.o cs_cholsol.o cs_compress.o cs_counts.o cs_cumsum.o cs_dfs.o
> cs_dmperm.o cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o
> cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o cs_house.o cs_ipvec.o cs_leaf.o
> cs_load.o cs_lsolve.o cs_ltsolve.o cs_lu.o cs_lusol.o cs_malloc.o
> cs_maxtrans.o cs_multiply.o cs_norm.o cs_permute.o cs_pinv.o cs_post.o
> cs_print.o cs_pvec.o cs_qr.o cs_qrsol.o cs_randperm.o cs_reach.o
> cs_scatter.o cs_scc.o cs_schol.o cs_spsolve.o cs_sqr.o cs_symperm.o
> cs_tdfs.o cs_transpose.o cs_updown.o cs_usolve.o cs_util.o cs_utsolve.o
> decomposition.o dgetv0.o distances.o dlaqrb.o dmout.o dnaitr.o dnapps.o
> dnaup2.o dnaupd.o dnconv.o dneigh.o dneupd.o dngets.o dqueue.o drl_graph.o
> drl_graph_3d.o drl_layout.o drl_layout_3d.o drl_parse.o dsaitr.o dsapps.o
> dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o
> dsortr.o dstatn.o dstats.o dstqrb.o dvout.o eigen.o error.o evolver_cit.o
> f2c_dummy.o fast_community.o feedback_arc_set.o flow.o foreign-dl-lexer.o
> foreign-dl-parser.o foreign-gml-lexer.o foreign-gml-parser.o
> foreign-graphml.o foreign-lgl-lexer.o foreign-lgl-parser.o
> foreign-ncol-lexer.o foreign-ncol-parser.o foreign-pajek-lexer.o
> foreign-pajek-parser.o foreign.o forestfire.o fortran_intrinsics.o games.o
> gengraph_box_list.o gengraph_degree_sequence.o gengraph_graph_molloy_hash.o
> gengraph_graph_molloy_optimized.o gengraph_mr-connected.o
> gengraph_powerlaw.o gengraph_random.o glpapi01.o glpapi02.o glpapi03.o
> glpapi04.o glpapi05.o glpapi06.o glpapi07.o glpapi08.o glpapi09.o glpapi10.o
> glpapi11.o glpapi12.o glpapi13.o glpapi14.o glpapi15.o glpapi16.o glpapi17.o
> glpapi18.o glpapi19.o glpavl.o glpbfd.o glpbfx.o glpcpx.o glpdmp.o glpdmx.o
> glpenv01.o glpenv02.o glpenv03.o glpenv04.o glpenv05.o glpenv06.o glpenv07.o
> glpenv08.o glpfhv.o glpgmp.o glphbm.o glpini01.o glpini02.o glpios01.o
> glpios02.o glpios03.o glpios04.o glpios05.o glpios06.o glpios07.o glpios08.o
> glpios09.o glpios10.o glpios11.o glpios12.o glpipm.o glpk_support.o
> glplib01.o glplib02.o glplib03.o glplpf.o glplpx01.o glplpx02.o glplpx03.o
> glpluf.o glplux.o glpmat.o glpmpl01.o glpmpl02.o glpmpl03.o glpmpl04.o
> glpmpl05.o glpmpl06.o glpmps.o glpnet01.o glpnet02.o glpnet03.o glpnet04.o
> glpnet05.o glpnet06.o glpnet07.o glpnet08.o glpnet09.o glpnpp01.o glpnpp02.o
> glpnpp03.o glpnpp04.o glpnpp05.o glpqmd.o glprgr.o glprng01.o glprng02.o
> glpscf.o glpscl.o glpsdf.o glpspm.o glpspx01.o glpspx02.o glpsql.o
> glpssx01.o glpssx02.o glptsp.o gml_tree.o heap.o igraph_buckets.o
> igraph_estack.o igraph_fixed_vectorlist.o igraph_grid.o igraph_hashtable.o
> igraph_heap.o igraph_hrg.o igraph_hrg_types.o igraph_marked_queue.o
> igraph_psumtree.o igraph_set.o igraph_stack.o igraph_strvector.o
> igraph_trie.o infomap.o infomap_FlowGraph.o infomap_Greedy.o infomap_Node.o
> interrupt.o iterators.o ivout.o lapack.o layout.o matching.o math.o matrix.o
> memory.o microscopic_update.o mixing.o motifs.o operators.o
> optimal_modularity.o other.o pottsmodel_2.o progress.o qsort.o qsort_r.o
> random.o revolver_cit.o revolver_grow.o revolver_ml_cit.o rinterface.o scg.o
> scg_approximate_methods.o scg_exact_scg.o scg_kmeans.o scg_optimal_method.o
> scg_utils.o second.o separators.o spanning_trees.o sparsemat.o
> spectral_properties.o spmatrix.o st-cuts.o statusbar.o
> structural_properties.o structure_generators.o sugiyama.o topology.o
> type_indexededgelist.o types.o vector.o vector_ptr.o version.o visitors.o
> walktrap.o walktrap_communities.o walktrap_graph.o walktrap_heap.o zeroin.o
> -lxml2 -lz -lm -lgmp -lifport -lifcore -limf -lsvml -lm -lipgo -lirc
> -lpthread -lirc_s -ldl -L/export/intel/Compiler/12.1/mkl/lib/intel64/
> -lmkl_intel_lp64 -lmkl_sequential -lmkl_lapack95_lp64 -lmkl_core -lifport
> -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
> foreign-lgl-parser.o: In function `stpcpy':
> /tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-lgl-parser.y:63:
> multiple definition of `stpcpy'
> foreign-gml-parser.o:/tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-gml-parser.y:65:
> first defined here
> foreign-ncol-parser.o: In function `stpcpy':
> /tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-ncol-parser.y:65:
> multiple definition of `stpcpy'
> foreign-gml-parser.o:/tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-gml-parser.y:65:
> first defined here
> foreign-pajek-parser.o: In function `stpcpy':
> /tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-pajek-parser.y:67:
> multiple definition of `stpcpy'
> foreign-gml-parser.o:/tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-gml-parser.y:65:
> first defined here
> make: *** [igraph.so] Error 1
> ERROR: compilation failed for package ‘igraph’
> * removing ‘/export/R-2.15.2/lib64/R/library/igraph’
> Any suggestions?
> Malcolm
> --
> Malcolm Tobias
> 314.362.1594
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help

Gabor Csardi <address@hidden>     MTA KFKI RMKI

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