lalsuite pycbc won't install - Ubuntu
I'm working through these instructions https://pycbc.org/pycbc/latest/html/install_lalsuite.html for installing pycbc which I need for my research, and I have some issues. Just under half way down that page, where it has
./00boot
./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-swig-python --disable-lalstochastic --disable-lalxml --disable-lalinference --disable-laldetchar --disable-lalapps
I get these messages after running the ./configure
line
checking whether PyArray_SetBaseObject is declared... yes
configure: error: SWIG version 2.0.12 or later is required
SWIG support can be disabled by using the --disable-swig configure option
configure: error: ./configure failed for lal
There's plenty more above it if anyone wants the whole thing.
I tried following these instructions http://www.linuxfromscratch.org/blfs/view/7.5/general/swig.html and https://help.dreamhost.com/hc/en-us/articles/215489188-How-to-install-a-newer-version-of-SWIG but that hasn't helped.
I'm now out of ideas and worried that if I keep trying random things I'll make it worse. Yesterday I reinstalled Ubuntu onto this computer, so there shouldn't be too much mess about it.
Cheers!
** Edit
If I try just a simple
pip install lalsuite pycbc
as following these instructions https://pycbc.org/pycbc/latest/html/install.html I get a seg fault:
Collecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pycbc
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting beautifulsoup4>=4.6.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/f8/c7/741c97d7366f4779ca73d244904978b43a81fd37d85fcf05ad19d472c1ce/beautifulsoup4-4.6.3-py2-none-any.whl
Collecting cython (from pycbc)
Using cached https://files.pythonhosted.org/packages/eb/b0/0069db01146b4810cbe2d7045ebbc80baca5470ee4b51b1e991eb90d8f07/Cython-0.29.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting jinja2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting emcee==2.2.1 (from pycbc)
Collecting requests>=1.2.1 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pillow (from pycbc)
Using cached https://files.pythonhosted.org/packages/9a/f6/3b3c82c5c75cae471e02fb584136168d732e17ae9db2d21c5dc82f9790f8/Pillow-5.3.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting mpld3>=0.3 (from pycbc)
Collecting kombine>=0.8.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/ce/70/d7eff8255247dd56b89f6547067ad418c10f71e796968f6208adbb68e032/kombine-0.8.3-py2.py3-none-any.whl
Collecting weave>=0.16.0 (from pycbc)
Collecting h5py>=2.5 (from pycbc)
Downloading https://files.pythonhosted.org/packages/53/08/27e4e9a369321862ffdce80ff1770553e9daec65d98befb2e14e7478b698/h5py-2.9.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
100% |████████████████████████████████| 2.8MB 453kB/s
Collecting Mako>=1.0.1 (from pycbc)
Collecting decorator>=3.4.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting astropy<3.0.0,>=2.0.3 (from pycbc)
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from jinja2->pycbc)
Using cached https://files.pythonhosted.org/packages/bc/3a/6bfd7b4b202fa33bdda8e4e3d3acc719f381fd730f9a0e7c5f34e845bd4d/MarkupSafe-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl
Collecting urllib3<1.25,>=1.21.1 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl
Collecting pytest<3.7,>=2.8 (from astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/d8/e9/73246a565c34c5f203dd78bc2382e0e93aa7a249cdaeba709099eb1bc701/pytest-3.6.4-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting pluggy<0.8,>=0.5 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/f5/f1/5a93c118663896d83f7bcbfb7f657ce1d0c0d617e6b4a443a53abcc658ca/pluggy-0.7.1-py2.py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3a/9a/9d878f8d885706e2530402de6417141129a943802c084238914fa6798d97/atomicwrites-1.2.1-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3e/c7/3da685ef117d42ac8d71af525208759742dd235f8094221fdaafcd3dba8f/py-1.7.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/fb/d3/77f337876600747ae307ea775ff264c5304a691941cd347382c7932c60ad/more_itertools-4.3.0-py2-none-any.whl
Collecting attrs>=17.4.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3a/e1/5f9023cc983f1a628a8c2fd051ad19e76ff7b142a0faf329336f9a62a514/attrs-18.2.0-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, enCollecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting six (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl enCollecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting six (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
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Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting idna>=2.1 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite
Segmentation fault (core dumped)
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting idna>=2.1 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite
Segmentation fault (core dumped) idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite, beautifulsoup4, cython, MarkupSafe, jinja2, emcee, chardet, certifi, urllib3, requests, pillow, mpld3, kombine, weave, h5py, Mako, decorator, pluggy, atomicwrites, py, funcsigs, more-itertools, attrs, pytest, astropy, pycbc
Segmentation fault (core dumped)
ubuntu python configure segmentation-fault
add a comment |
I'm working through these instructions https://pycbc.org/pycbc/latest/html/install_lalsuite.html for installing pycbc which I need for my research, and I have some issues. Just under half way down that page, where it has
./00boot
./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-swig-python --disable-lalstochastic --disable-lalxml --disable-lalinference --disable-laldetchar --disable-lalapps
I get these messages after running the ./configure
line
checking whether PyArray_SetBaseObject is declared... yes
configure: error: SWIG version 2.0.12 or later is required
SWIG support can be disabled by using the --disable-swig configure option
configure: error: ./configure failed for lal
There's plenty more above it if anyone wants the whole thing.
I tried following these instructions http://www.linuxfromscratch.org/blfs/view/7.5/general/swig.html and https://help.dreamhost.com/hc/en-us/articles/215489188-How-to-install-a-newer-version-of-SWIG but that hasn't helped.
I'm now out of ideas and worried that if I keep trying random things I'll make it worse. Yesterday I reinstalled Ubuntu onto this computer, so there shouldn't be too much mess about it.
Cheers!
** Edit
If I try just a simple
pip install lalsuite pycbc
as following these instructions https://pycbc.org/pycbc/latest/html/install.html I get a seg fault:
Collecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pycbc
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting beautifulsoup4>=4.6.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/f8/c7/741c97d7366f4779ca73d244904978b43a81fd37d85fcf05ad19d472c1ce/beautifulsoup4-4.6.3-py2-none-any.whl
Collecting cython (from pycbc)
Using cached https://files.pythonhosted.org/packages/eb/b0/0069db01146b4810cbe2d7045ebbc80baca5470ee4b51b1e991eb90d8f07/Cython-0.29.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting jinja2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting emcee==2.2.1 (from pycbc)
Collecting requests>=1.2.1 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pillow (from pycbc)
Using cached https://files.pythonhosted.org/packages/9a/f6/3b3c82c5c75cae471e02fb584136168d732e17ae9db2d21c5dc82f9790f8/Pillow-5.3.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting mpld3>=0.3 (from pycbc)
Collecting kombine>=0.8.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/ce/70/d7eff8255247dd56b89f6547067ad418c10f71e796968f6208adbb68e032/kombine-0.8.3-py2.py3-none-any.whl
Collecting weave>=0.16.0 (from pycbc)
Collecting h5py>=2.5 (from pycbc)
Downloading https://files.pythonhosted.org/packages/53/08/27e4e9a369321862ffdce80ff1770553e9daec65d98befb2e14e7478b698/h5py-2.9.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
100% |████████████████████████████████| 2.8MB 453kB/s
Collecting Mako>=1.0.1 (from pycbc)
Collecting decorator>=3.4.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting astropy<3.0.0,>=2.0.3 (from pycbc)
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from jinja2->pycbc)
Using cached https://files.pythonhosted.org/packages/bc/3a/6bfd7b4b202fa33bdda8e4e3d3acc719f381fd730f9a0e7c5f34e845bd4d/MarkupSafe-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl
Collecting urllib3<1.25,>=1.21.1 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl
Collecting pytest<3.7,>=2.8 (from astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/d8/e9/73246a565c34c5f203dd78bc2382e0e93aa7a249cdaeba709099eb1bc701/pytest-3.6.4-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting pluggy<0.8,>=0.5 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/f5/f1/5a93c118663896d83f7bcbfb7f657ce1d0c0d617e6b4a443a53abcc658ca/pluggy-0.7.1-py2.py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3a/9a/9d878f8d885706e2530402de6417141129a943802c084238914fa6798d97/atomicwrites-1.2.1-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3e/c7/3da685ef117d42ac8d71af525208759742dd235f8094221fdaafcd3dba8f/py-1.7.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/fb/d3/77f337876600747ae307ea775ff264c5304a691941cd347382c7932c60ad/more_itertools-4.3.0-py2-none-any.whl
Collecting attrs>=17.4.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3a/e1/5f9023cc983f1a628a8c2fd051ad19e76ff7b142a0faf329336f9a62a514/attrs-18.2.0-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, enCollecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting six (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl enCollecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting six (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting idna>=2.1 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite
Segmentation fault (core dumped)
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting idna>=2.1 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite
Segmentation fault (core dumped) idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite, beautifulsoup4, cython, MarkupSafe, jinja2, emcee, chardet, certifi, urllib3, requests, pillow, mpld3, kombine, weave, h5py, Mako, decorator, pluggy, atomicwrites, py, funcsigs, more-itertools, attrs, pytest, astropy, pycbc
Segmentation fault (core dumped)
ubuntu python configure segmentation-fault
add a comment |
I'm working through these instructions https://pycbc.org/pycbc/latest/html/install_lalsuite.html for installing pycbc which I need for my research, and I have some issues. Just under half way down that page, where it has
./00boot
./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-swig-python --disable-lalstochastic --disable-lalxml --disable-lalinference --disable-laldetchar --disable-lalapps
I get these messages after running the ./configure
line
checking whether PyArray_SetBaseObject is declared... yes
configure: error: SWIG version 2.0.12 or later is required
SWIG support can be disabled by using the --disable-swig configure option
configure: error: ./configure failed for lal
There's plenty more above it if anyone wants the whole thing.
I tried following these instructions http://www.linuxfromscratch.org/blfs/view/7.5/general/swig.html and https://help.dreamhost.com/hc/en-us/articles/215489188-How-to-install-a-newer-version-of-SWIG but that hasn't helped.
I'm now out of ideas and worried that if I keep trying random things I'll make it worse. Yesterday I reinstalled Ubuntu onto this computer, so there shouldn't be too much mess about it.
Cheers!
** Edit
If I try just a simple
pip install lalsuite pycbc
as following these instructions https://pycbc.org/pycbc/latest/html/install.html I get a seg fault:
Collecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pycbc
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting beautifulsoup4>=4.6.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/f8/c7/741c97d7366f4779ca73d244904978b43a81fd37d85fcf05ad19d472c1ce/beautifulsoup4-4.6.3-py2-none-any.whl
Collecting cython (from pycbc)
Using cached https://files.pythonhosted.org/packages/eb/b0/0069db01146b4810cbe2d7045ebbc80baca5470ee4b51b1e991eb90d8f07/Cython-0.29.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting jinja2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting emcee==2.2.1 (from pycbc)
Collecting requests>=1.2.1 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pillow (from pycbc)
Using cached https://files.pythonhosted.org/packages/9a/f6/3b3c82c5c75cae471e02fb584136168d732e17ae9db2d21c5dc82f9790f8/Pillow-5.3.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting mpld3>=0.3 (from pycbc)
Collecting kombine>=0.8.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/ce/70/d7eff8255247dd56b89f6547067ad418c10f71e796968f6208adbb68e032/kombine-0.8.3-py2.py3-none-any.whl
Collecting weave>=0.16.0 (from pycbc)
Collecting h5py>=2.5 (from pycbc)
Downloading https://files.pythonhosted.org/packages/53/08/27e4e9a369321862ffdce80ff1770553e9daec65d98befb2e14e7478b698/h5py-2.9.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
100% |████████████████████████████████| 2.8MB 453kB/s
Collecting Mako>=1.0.1 (from pycbc)
Collecting decorator>=3.4.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting astropy<3.0.0,>=2.0.3 (from pycbc)
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from jinja2->pycbc)
Using cached https://files.pythonhosted.org/packages/bc/3a/6bfd7b4b202fa33bdda8e4e3d3acc719f381fd730f9a0e7c5f34e845bd4d/MarkupSafe-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl
Collecting urllib3<1.25,>=1.21.1 (from requests>=1.2.1->pycbc)
Using cached https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl
Collecting pytest<3.7,>=2.8 (from astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/d8/e9/73246a565c34c5f203dd78bc2382e0e93aa7a249cdaeba709099eb1bc701/pytest-3.6.4-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting pluggy<0.8,>=0.5 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/f5/f1/5a93c118663896d83f7bcbfb7f657ce1d0c0d617e6b4a443a53abcc658ca/pluggy-0.7.1-py2.py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3a/9a/9d878f8d885706e2530402de6417141129a943802c084238914fa6798d97/atomicwrites-1.2.1-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3e/c7/3da685ef117d42ac8d71af525208759742dd235f8094221fdaafcd3dba8f/py-1.7.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/fb/d3/77f337876600747ae307ea775ff264c5304a691941cd347382c7932c60ad/more_itertools-4.3.0-py2-none-any.whl
Collecting attrs>=17.4.0 (from pytest<3.7,>=2.8->astropy<3.0.0,>=2.0.3->pycbc)
Using cached https://files.pythonhosted.org/packages/3a/e1/5f9023cc983f1a628a8c2fd051ad19e76ff7b142a0faf329336f9a62a514/attrs-18.2.0-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, enCollecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting six (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl enCollecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting six (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting cryptography>=2.2.1 (from pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/7f/ba/383b51cc26e3141c689ce988814385c7659f5ba01c4b5f2de38233010b5f/cryptography-2.4.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting setuptools (from kiwisolver>=1.0.1->matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/37/06/754589caf971b0d2d48f151c2586f62902d93dc908e2fd9b9b9f6aa3c9dd/setuptools-40.6.3-py2.py3-none-any.whl
Collecting enum34; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting idna>=2.1 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite
Segmentation fault (core dumped)
Collecting cffi!=1.11.3,>=1.7 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/dd/3e7a1e1280e7d767bd3fa15791759c91ec19058ebe31217fe66f3e9a8c49/cffi-1.11.5-cp27-cp27mu-manylinux1_x86_64.whl
Collecting asn1crypto>=0.21.0 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting idna>=2.1 (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting ipaddress; python_version < "3" (from cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.7->cryptography>=2.2.1->pyOpenSSL->lscsoft-glue->lalsuite)
Installing collected packages: ligo-common, six, ligo-segments, enum34, pycparser, cffi, asn1crypto, idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite
Segmentation fault (core dumped) idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite, beautifulsoup4, cython, MarkupSafe, jinja2, emcee, chardet, certifi, urllib3, requests, pillow, mpld3, kombine, weave, h5py, Mako, decorator, pluggy, atomicwrites, py, funcsigs, more-itertools, attrs, pytest, astropy, pycbc
Segmentation fault (core dumped)
ubuntu python configure segmentation-fault
I'm working through these instructions https://pycbc.org/pycbc/latest/html/install_lalsuite.html for installing pycbc which I need for my research, and I have some issues. Just under half way down that page, where it has
./00boot
./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-swig-python --disable-lalstochastic --disable-lalxml --disable-lalinference --disable-laldetchar --disable-lalapps
I get these messages after running the ./configure
line
checking whether PyArray_SetBaseObject is declared... yes
configure: error: SWIG version 2.0.12 or later is required
SWIG support can be disabled by using the --disable-swig configure option
configure: error: ./configure failed for lal
There's plenty more above it if anyone wants the whole thing.
I tried following these instructions http://www.linuxfromscratch.org/blfs/view/7.5/general/swig.html and https://help.dreamhost.com/hc/en-us/articles/215489188-How-to-install-a-newer-version-of-SWIG but that hasn't helped.
I'm now out of ideas and worried that if I keep trying random things I'll make it worse. Yesterday I reinstalled Ubuntu onto this computer, so there shouldn't be too much mess about it.
Cheers!
** Edit
If I try just a simple
pip install lalsuite pycbc
as following these instructions https://pycbc.org/pycbc/latest/html/install.html I get a seg fault:
Collecting lalsuite
Using cached https://files.pythonhosted.org/packages/c7/d3/d77caabf6f5e4000637624c9613a6ed21bf04bdb8478a215ac3600d4b13f/lalsuite-6.49-cp27-cp27mu-manylinux1_x86_64.whl
Collecting pycbc
Collecting ligo-segments (from lalsuite)
Collecting lscsoft-glue (from lalsuite)
Collecting matplotlib (from lalsuite)
Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scipy (from lalsuite)
Using cached https://files.pythonhosted.org/packages/45/d1/7c2b33a5daee3d67752d043fe7e1476c4465788b0b6e59367fd71fdf684a/scipy-1.2.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-dateutil (from lalsuite)
Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl
Collecting numpy>=1.7 (from lalsuite)
Using cached https://files.pythonhosted.org/packages/de/37/fe7db552f4507f379d81dcb78e58e05030a8941757b1f664517d581b5553/numpy-1.15.4-cp27-cp27mu-manylinux1_x86_64.whl
Collecting beautifulsoup4>=4.6.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/f8/c7/741c97d7366f4779ca73d244904978b43a81fd37d85fcf05ad19d472c1ce/beautifulsoup4-4.6.3-py2-none-any.whl
Collecting cython (from pycbc)
Using cached https://files.pythonhosted.org/packages/eb/b0/0069db01146b4810cbe2d7045ebbc80baca5470ee4b51b1e991eb90d8f07/Cython-0.29.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting jinja2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting emcee==2.2.1 (from pycbc)
Collecting requests>=1.2.1 (from pycbc)
Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pycbc)
Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting pillow (from pycbc)
Using cached https://files.pythonhosted.org/packages/9a/f6/3b3c82c5c75cae471e02fb584136168d732e17ae9db2d21c5dc82f9790f8/Pillow-5.3.0-cp27-cp27mu-manylinux1_x86_64.whl
Collecting mpld3>=0.3 (from pycbc)
Collecting kombine>=0.8.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/ce/70/d7eff8255247dd56b89f6547067ad418c10f71e796968f6208adbb68e032/kombine-0.8.3-py2.py3-none-any.whl
Collecting weave>=0.16.0 (from pycbc)
Collecting h5py>=2.5 (from pycbc)
Downloading https://files.pythonhosted.org/packages/53/08/27e4e9a369321862ffdce80ff1770553e9daec65d98befb2e14e7478b698/h5py-2.9.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
100% |████████████████████████████████| 2.8MB 453kB/s
Collecting Mako>=1.0.1 (from pycbc)
Collecting decorator>=3.4.2 (from pycbc)
Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting astropy<3.0.0,>=2.0.3 (from pycbc)
Collecting ligo-common (from ligo-segments->lalsuite)
Using cached https://files.pythonhosted.org/packages/a6/9c/1fbe176feea9abad5c0f3fa090dcffccf44bbcba0f0c754b03d8fea1a36e/ligo_common-1.0.3-py2.py3-none-any.whl
Collecting pyOpenSSL (from lscsoft-glue->lalsuite)
Using cached https://files.pythonhosted.org/packages/96/af/9d29e6bd40823061aea2e0574ccb2fcf72bfd6130ce53d32773ec375458c/pyOpenSSL-18.0.0-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl
Collecting backports.functools-lru-cache (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->lalsuite)
Collecting pytz (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->lalsuite)
Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib->lalsuite)
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Segmentation fault (core dumped)
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Segmentation fault (core dumped) idna, ipaddress, cryptography, pyOpenSSL, numpy, lscsoft-glue, pyparsing, backports.functools-lru-cache, subprocess32, python-dateutil, pytz, setuptools, kiwisolver, cycler, matplotlib, scipy, lalsuite, beautifulsoup4, cython, MarkupSafe, jinja2, emcee, chardet, certifi, urllib3, requests, pillow, mpld3, kombine, weave, h5py, Mako, decorator, pluggy, atomicwrites, py, funcsigs, more-itertools, attrs, pytest, astropy, pycbc
Segmentation fault (core dumped)
ubuntu python configure segmentation-fault
ubuntu python configure segmentation-fault
edited yesterday
asked 2 days ago
user1153070
814
814
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1 Answer
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votes
If you just want to install lalsuite and not develop it, have you considered installing from pip as pip install lalsuite
?
If you do want to build from source and want to install swig, it might be easier to use your package manager since swig3 is available.
https://packages.ubuntu.com/cosmic/swig
Something like apt-get install swig3
.
New contributor
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
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If you just want to install lalsuite and not develop it, have you considered installing from pip as pip install lalsuite
?
If you do want to build from source and want to install swig, it might be easier to use your package manager since swig3 is available.
https://packages.ubuntu.com/cosmic/swig
Something like apt-get install swig3
.
New contributor
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
add a comment |
If you just want to install lalsuite and not develop it, have you considered installing from pip as pip install lalsuite
?
If you do want to build from source and want to install swig, it might be easier to use your package manager since swig3 is available.
https://packages.ubuntu.com/cosmic/swig
Something like apt-get install swig3
.
New contributor
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
add a comment |
If you just want to install lalsuite and not develop it, have you considered installing from pip as pip install lalsuite
?
If you do want to build from source and want to install swig, it might be easier to use your package manager since swig3 is available.
https://packages.ubuntu.com/cosmic/swig
Something like apt-get install swig3
.
New contributor
If you just want to install lalsuite and not develop it, have you considered installing from pip as pip install lalsuite
?
If you do want to build from source and want to install swig, it might be easier to use your package manager since swig3 is available.
https://packages.ubuntu.com/cosmic/swig
Something like apt-get install swig3
.
New contributor
New contributor
answered 2 days ago
Alex Nitz
1
1
New contributor
New contributor
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
add a comment |
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
That was the first thing I tried.. I don't have the computer with me right now though so I can't say why that failed
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
And I'm not interested in developing anything, I just want to use it.
– user1153070
yesterday
add a comment |
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