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Question: Libgomp error in IHW
1
gravatar for Kipper Fletez-Brant
3 months ago by
United States
Kipper Fletez-Brant150 wrote:

I am running IHW in a GWAS setting and after 2 days of processing, I get the following error message:

libgomp: Thread creation failed: Resource temporarily unavailable

When I Google this error, it seems that it is coming somehow from Lsymphony which IHW calls.  While I see an option in IHW that allows me to set a solver, I am wondering how to actually fix this error.

I might as well note here that if I try to set lp_solver="gurobi", I get the error message:

Error in gurobi(model, params) : could not find function "gurobi"

My session info is:

R version 3.4.3 Patched (2018-01-20 r74142)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.9 (Santiago)

Matrix products: default
BLAS: R/3.4.x/lib64/R/lib/libRblas.so
LAPACK: R/3.4.x/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices datasets  utils    
[8] methods   base     

other attached packages:
 [1] EBImage_4.20.1                    bnbc_1.0.0                       
 [3] lmerTest_2.0-36                   lme4_1.1-15                      
 [5] preprocessCore_1.40.0             BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [7] BSgenome_1.46.0                   rtracklayer_1.38.3               
 [9] Biostrings_2.46.0                 XVector_0.18.0                   
[11] IHW_1.6.0                         Matrix_1.2-12                    
[13] readr_1.1.1                       SummarizedExperiment_1.8.1       
[15] DelayedArray_0.4.1                Biobase_2.38.0                   
[17] GenomicRanges_1.30.3              GenomeInfoDb_1.14.0              
[19] IRanges_2.12.0                    S4Vectors_0.16.0                 
[21] BiocGenerics_0.24.0               data.table_1.10.4-3              
[23] matrixStats_0.53.1                scales_0.5.0                     
[25] tidyr_0.8.0                       dplyr_0.7.4                      
[27] magrittr_1.5                      qvalue_2.10.0                    

loaded via a namespace (and not attached):
 [1] nlme_3.1-131             bitops_1.0-6             bit64_0.9-7             
 [4] RColorBrewer_1.1-2       tools_3.4.3              backports_1.1.2         
 [7] R6_2.2.2                 rpart_4.1-12             mgcv_1.8-22             
[10] Hmisc_4.1-1              DBI_0.8                  lazyeval_0.2.1          
[13] colorspace_1.3-2         nnet_7.3-12              gridExtra_2.3           
[16] bit_1.1-12               compiler_3.4.3           fdrtool_1.2.15          
[19] htmlTable_1.11.2         slam_0.1-42              checkmate_1.8.5         
[22] genefilter_1.60.0        tiff_0.1-5               stringr_1.3.0           
[25] digest_0.6.15            Rsamtools_1.30.0         fftwtools_0.9-8         
[28] foreign_0.8-69           minqa_1.2.4              jpeg_0.1-8              
[31] base64enc_0.1-3          pkgconfig_2.0.1          htmltools_0.3.6         
[34] lpsymphony_1.7.1         limma_3.34.9             htmlwidgets_1.0         
[37] rlang_0.2.0              RSQLite_2.0              rstudioapi_0.7          
[40] bindr_0.1                BiocParallel_1.12.0      acepack_1.4.1           
[43] RCurl_1.95-4.10          GenomeInfoDbData_1.0.0   Formula_1.2-2           
[46] Rcpp_0.12.15             munsell_0.4.3            abind_1.4-5             
[49] stringi_1.1.6            MASS_7.3-48              zlibbioc_1.24.0         
[52] plyr_1.8.4               blob_1.1.0               grid_3.4.3              
[55] lattice_0.20-35          splines_3.4.3            annotate_1.56.1         
[58] hms_0.4.1                locfit_1.5-9.1           knitr_1.20              
[61] pillar_1.2.1             reshape2_1.4.3           XML_3.98-1.10           
[64] glue_1.2.0               latticeExtra_0.6-28      png_0.1-7               
[67] nloptr_1.0.4             gtable_0.2.0             purrr_0.2.4             
[70] assertthat_0.2.0         ggplot2_2.2.1            xtable_1.8-2            
[73] survival_2.41-3          tibble_1.4.2             memoise_1.1.0           
[76] GenomicAlignments_1.14.1 AnnotationDbi_1.40.0     bindrcpp_0.2            
[79] cluster_2.0.6            sva_3.26.0              

 

ihw
ADD COMMENTlink modified 3 months ago by vladislav.kim10 • written 3 months ago by Kipper Fletez-Brant150
0
gravatar for Nikos Ignatiadis
3 months ago by
Heidelberg
Nikos Ignatiadis130 wrote:

Hello! Indeed this appears to be related to the parallelization in Lpsymphony. Can you give some more context about your problem? How many p-values do you have and what are the covariates? Furthermore, as a basic sanity check, can you run the IHW examples (either in the documentation or the vignette) on the computing environment from which you get the error?

Regarding Gurobi, you would have to follow the instructions at their website (http://www.gurobi.com/) to install it. It is a commercial solver, which also offers free academic licenses. Nevertheless, I hope we can fix this issue with the default open source solver!

ADD COMMENTlink written 3 months ago by Nikos Ignatiadis130

We have been using the package successfully quite a few times, so I don't think it is a basic issue. It could depend on this exact set of p-values.  I think we have a LOT of p-values for this application, but I will let Kipper speak to the details here.

ADD REPLYlink written 3 months ago by Kasper Daniel Hansen6.3k
0
gravatar for vladislav.kim
3 months ago by
Germany
vladislav.kim10 wrote:

Hey,

the error indeed originates from upsteram of IHW in lpsymphony. By deault `lpsymphony` is compiled with --enable-openmp flag. Do you make targeted use of OpenMP threading?

Vlad

 

 

 

ADD COMMENTlink written 3 months ago by vladislav.kim10
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