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Install issues

Open slschnorr opened this issue 4 years ago • 6 comments

Expected Behavior

I'm having issues installing plass using all options. I work in CentOS 8 x86_64

Current Behavior

  1. Install from bioconda appears to succeed but then the plass executable does not exist

  2. Install from the static file results in: --2022-01-14 09:04:13-- https://mmseqs.com/plass/plass-static_sse41.tar.gz Resolving mmseqs.com (mmseqs.com)... 141.5.100.26 Connecting to mmseqs.com (mmseqs.com)|141.5.100.26|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2022-01-14 09:04:14 ERROR 404: Not Found.

  3. Install from git clone errors during make with: make -j 4 && make install Consolidate compiler generated dependencies of target microtar Consolidate compiler generated dependencies of target ksw2 Consolidate compiler generated dependencies of target cacode Consolidate compiler generated dependencies of target alp [ 2%] Built target microtar [ 2%] Built target ksw2 [ 2%] Built target cacode [ 7%] Built target alp [ 7%] Building C object lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o [ 7%] Generating ../generated/VTML80.out.h [ 7%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/entropy_common.c.o [ 7%] Generating ../generated/assemble.sh.h : invalid option make[2]: *** [lib/mmseqs/data/CMakeFiles/generated.dir/build.make:159: lib/mmseqs/generated/VTML80.out.h] Error 1 make[1]: *** [CMakeFiles/Makefile2:803: lib/mmseqs/data/CMakeFiles/generated.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... : invalid option make[2]: *** [data/CMakeFiles/local-generated.dir/build.make:81: generated/assemble.sh.h] Error 1 make[2]: *** Waiting for unfinished jobs.... [ 7%] Generating ../generated/nuclassemble.sh.h [ 7%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/fse_decompress.c.o : invalid option make[2]: *** [data/CMakeFiles/local-generated.dir/build.make:97: generated/nuclassemble.sh.h] Error 1 make[1]: *** [CMakeFiles/Makefile2:861: data/CMakeFiles/local-generated.dir/all] Error 2 [ 8%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/threading.c.o [ 8%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/pool.c.o [ 8%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/zstd_common.c.o [ 9%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/error_private.c.o [ 9%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/hist.c.o [ 9%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/xxhash.c.o [ 10%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/fse_compress.c.o [ 11%] Linking C static library libtinyexpr.a [ 11%] Built target tinyexpr [ 11%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/huf_compress.c.o [ 12%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_compress.c.o [ 12%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstdmt_compress.c.o [ 12%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_fast.c.o [ 13%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_double_fast.c.o [ 13%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_lazy.c.o [ 13%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_opt.c.o [ 14%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_ldm.c.o [ 14%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/huf_decompress.c.o [ 14%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/zstd_decompress.c.o [ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/zstd_decompress_block.c.o [ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/zstd_ddict.c.o [ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/cover.c.o [ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/fastcover.c.o [ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/divsufsort.c.o [ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/zdict.c.o [ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/deprecated/zbuff_common.c.o [ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/deprecated/zbuff_compress.c.o [ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/deprecated/zbuff_decompress.c.o [ 18%] Linking C static library libzstd.a [ 18%] Built target libzstd_static make: *** [Makefile:136: all] Error 2

Context

lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 48 On-line CPU(s) list: 0-47 Thread(s) per core: 2 Core(s) per socket: 12 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 62 Model name: Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz Stepping: 4 CPU MHz: 3500.000 CPU max MHz: 3500.0000 CPU min MHz: 1200.0000 BogoMIPS: 5387.14 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 30720K NUMA node0 CPU(s): 0-11,24-35 NUMA node1 CPU(s): 12-23,36-47

slschnorr avatar Jan 14 '22 14:01 slschnorr

We changed the naming scheme of the files on the download server and forgot to update the readme:

You can find the SSE4.1 Linux binary at: https://mmseqs.com/plass/plass-linux-sse41.tar.gz

To compile from source you need to have either xxd (usually from a system package like vim-common) or if that doesn't exist then it will fall back to a perl script.

milot-mirdita avatar Jan 14 '22 16:01 milot-mirdita

Hi Thanks that worked and I got it installed. But I do have xxd, so I'm confused why compiling from source failed, especially if it should fall back to a perl script.

slschnorr avatar Jan 14 '22 17:01 slschnorr

If you have the cmake build directory still could you show the output of the following files:

cat CMakeFiles/CMakeOutput.log CMakeFiles/CMakeError.log

milot-mirdita avatar Jan 14 '22 17:01 milot-mirdita

plass_CMakelogs.txt

slschnorr avatar Jan 14 '22 17:01 slschnorr

Hm that didn't help much, could you make a new build folder, run cmake again from this fresh build folder and post its output? I can't reproduce the issue :/

milot-mirdita avatar Jan 14 '22 18:01 milot-mirdita

Sure :) plass_CMakelogs2.txt

slschnorr avatar Jan 14 '22 20:01 slschnorr